From 9795ac65043384d8e9ab353433100fb5ea2c9e93 Mon Sep 17 00:00:00 2001 From: David DeTomaso Date: Sat, 16 May 2020 15:41:55 -0700 Subject: [PATCH 01/62] Fix for #77 Also, some documentation fixes (use accessor methods) --- R/Utilities.R | 2 +- docs/articles/VISION-vignette.html | 29 +++++++++++++-------------- docs/pkgdown.yml | 2 +- docs/reference/matrix_wilcox_cpp.html | 2 +- man/matrix_wilcox_cpp.Rd | 2 +- vignettes/VISION-vignette.Rmd | 14 ++++++------- 6 files changed, 24 insertions(+), 27 deletions(-) diff --git a/R/Utilities.R b/R/Utilities.R index de97656c..ca8d1aea 100644 --- a/R/Utilities.R +++ b/R/Utilities.R @@ -245,7 +245,7 @@ matrix_wilcox <- function(ranks, cluster_ii, #' @return pval - numeric vector, pvalue for each row #' @return stat - numeric vector, test statistic (AUC) for each row matrix_wilcox_cpp <- function(data, cluster_num, cluster_denom, - jobs = getOption("mc.cores", 2L)) { + jobs = getOption("mc.cores", 1L)) { # Subsetting individual rows is bad with a sparse matrix # instead we subset chunks at a time diff --git a/docs/articles/VISION-vignette.html b/docs/articles/VISION-vignette.html index 3e98a619..7debab68 100644 --- a/docs/articles/VISION-vignette.html +++ b/docs/articles/VISION-vignette.html @@ -175,9 +175,10 @@

Running an Analysis

To run an analysis, simply call the analyze function:

# Set the number of threads when running parallel computations
-options(mc.cores = 2)
-
-vis <- analyze(vis)
+# On Windows, this must either be omitted or set to 1 +options(mc.cores = 2) + +vis <- analyze(vis)

@@ -187,19 +188,17 @@

This will launch a browser running the interactive report.

Other options (port, host, browser) can be provided to control how this occurs. For example, if you are launching a report on a remote server (such as an AWS instance) and want to make it accessible to others, run this with host="0.0.0.0", some selected port number (e.g. port=8888), and browser=FALSE (so a browser isn’t auto-opened). Then the report should be available at “<your instance IP address>:8888”. (Note: You will also likely need to enable inbound traffic on your selected port for this to work correctly).

Alternately, you can work with the VISION object directly in R. For example:

-
# Display autocorrelation coefficients for signatures
-head(vis@SigConsistencyScores@sigProjMatrix)
+
-
For more details on the structure of the VISION object see XXX.

+
+# Plot signature scores for a signature of interest
+tsne <- getProjections(vis)[["tSNE30"]]
+sigScores <- getSignatureScores(vis)[, "HALLMARK_INTERFERON_GAMMA_RESPONSE"]
+
+library(ggplot2)
+ggplot() + aes(x=tsne[, 1], y=tsne[, 2], color=sigScores) + geom_point()
+

For more details on accessing computed data within the VISION object, see the References page.

diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 23a1084f..934aa02d 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -1,4 +1,4 @@ -pandoc: 2.3.1 +pandoc: 2.2.3.2 pkgdown: 1.3.0.9000 pkgdown_sha: ~ articles: diff --git a/docs/reference/matrix_wilcox_cpp.html b/docs/reference/matrix_wilcox_cpp.html index 4ac5e5e3..10f03513 100644 --- a/docs/reference/matrix_wilcox_cpp.html +++ b/docs/reference/matrix_wilcox_cpp.html @@ -157,7 +157,7 @@

C++ wilcox rank-sums test

matrix_wilcox_cpp(data, cluster_num, cluster_denom,
-  jobs = getOption("mc.cores", 2L))
+ jobs = getOption("mc.cores", 1L))

Arguments

diff --git a/man/matrix_wilcox_cpp.Rd b/man/matrix_wilcox_cpp.Rd index 5def2b35..96b49dff 100644 --- a/man/matrix_wilcox_cpp.Rd +++ b/man/matrix_wilcox_cpp.Rd @@ -5,7 +5,7 @@ \title{C++ wilcox rank-sums test} \usage{ matrix_wilcox_cpp(data, cluster_num, cluster_denom, - jobs = getOption("mc.cores", 2L)) + jobs = getOption("mc.cores", 1L)) } \arguments{ \item{data}{matrix of values, each row representing a separate variable} diff --git a/vignettes/VISION-vignette.Rmd b/vignettes/VISION-vignette.Rmd index 93e4738d..ff5de530 100644 --- a/vignettes/VISION-vignette.Rmd +++ b/vignettes/VISION-vignette.Rmd @@ -97,6 +97,7 @@ To run an analysis, simply call the analyze function: ```{r, collapse=T, message=F, eval=F} # Set the number of threads when running parallel computations +# On Windows, this must either be omitted or set to 1 options(mc.cores = 2) vis <- analyze(vis) @@ -117,22 +118,19 @@ Other options (port, host, browser) can be provided to control how this occurs. Alternately, you can work with the VISION object directly in R. For example: ```{r, collapse=T, message=F, results=F, eval=F} -# Display autocorrelation coefficients for signatures -head(vis@SigConsistencyScores@sigProjMatrix) +# Display autocorrelation coefficients, p-values for signatures +head(getSignatureAutocorrelation(vis)) -# View autocorrelation empirical p-values -head(vis@SigConsistencyScores@emp_pMatrix) # Plot signature scores for a signature of interest -tsne <- vis@Projections$tSNE30 -sigScores <- vis@sigScores[, "HALLMARK_INTERFERON_GAMMA_RESPONSE"] +tsne <- getProjections(vis)[["tSNE30"]] +sigScores <- getSignatureScores(vis)[, "HALLMARK_INTERFERON_GAMMA_RESPONSE"] library(ggplot2) ggplot() + aes(x=tsne[, 1], y=tsne[, 2], color=sigScores) + geom_point() ``` -For more details on the structure of the VISION object see XXX. - +For more details on accessing computed data within the VISION object, see the [References](https://yoseflab.github.io/VISION/reference/index.html) page. ## Customizing the Latent Space From 730d2c21361f1569ad9195a5d68cad6d74b1ce6c Mon Sep 17 00:00:00 2001 From: Matthew Jones Date: Tue, 20 Oct 2020 15:43:30 -0700 Subject: [PATCH 02/62] sparse gene importance bug fix --- R/AnalysisFunctions.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/AnalysisFunctions.R b/R/AnalysisFunctions.R index 2712dcec..6f0253e5 100644 --- a/R/AnalysisFunctions.R +++ b/R/AnalysisFunctions.R @@ -457,7 +457,7 @@ evalSigGeneImportanceSparse <- function(sigScores, sigData, normExpr){ geneCov <- geneCov[, 1] geneCov <- geneCov[names(genes)] - geneCov <- geneCov * genes # invert sign for negative genes + geneCov <- geneCov * unlist(genes) # invert sign for negative genes return(geneCov) } From eebfe5c70c0c51b258ed510bfef3e56a090c0cc1 Mon Sep 17 00:00:00 2001 From: Matthew Jones Date: Tue, 20 Oct 2020 17:43:10 -0700 Subject: [PATCH 03/62] color scale to red for gene expression --- inst/html_output/src/ColorScatterPlotly.js | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/inst/html_output/src/ColorScatterPlotly.js b/inst/html_output/src/ColorScatterPlotly.js index ab8f495f..bf3cd4f6 100644 --- a/inst/html_output/src/ColorScatterPlotly.js +++ b/inst/html_output/src/ColorScatterPlotly.js @@ -157,8 +157,9 @@ ColorScatter.prototype.setData = function(object) } else { colorscale = [ [0, '#d8d8d8'], - [0.5, '#395252'], - [1, '#000000'], + // [0.5, '#395252'], + [1, '#b4382d'], + //[1, '#000000'], ] } From 6e15d788a19e8ae450843ec84e300e7694637bd2 Mon Sep 17 00:00:00 2001 From: Matthew Jones Date: Tue, 20 Oct 2020 18:30:07 -0700 Subject: [PATCH 04/62] color scale for gene expr from gray to red --- inst/html_output/src/ColorScatterPlotly.js | 15 ++++++++++----- 1 file changed, 10 insertions(+), 5 deletions(-) diff --git a/inst/html_output/src/ColorScatterPlotly.js b/inst/html_output/src/ColorScatterPlotly.js index bf3cd4f6..4704abe2 100644 --- a/inst/html_output/src/ColorScatterPlotly.js +++ b/inst/html_output/src/ColorScatterPlotly.js @@ -156,10 +156,11 @@ ColorScatter.prototype.setData = function(object) colorscale = 'Viridis' } else { colorscale = [ - [0, '#d8d8d8'], + //[0, '#d8d8d8'], // [0.5, '#395252'], - [1, '#b4382d'], //[1, '#000000'], + [0, '#d8d8d8'], + [1, '#952E25'], ] } @@ -434,7 +435,7 @@ ColorScatter.prototype.getLayout = function() { title: titleOpt, hovermode: 'closest', paper_bgcolor: 'rgba(255, 255, 255, 0)', - plot_bgcolor: '#eeeeee', + plot_bgcolor: '#ffffff', dragmode: 'pan', legend: { xanchor: 'right', @@ -457,14 +458,18 @@ ColorScatter.prototype.getLayout = function() { range: [this.currentZoom.xmin, this.currentZoom.xmax], title: { 'text': xlabel, - } + }, + showgrid: false, + showline: true, }, yaxis: { zeroline: false, range: [this.currentZoom.ymin, this.currentZoom.ymax], title: { 'text': ylabel, - } + }, + showgrid: false, + showline: true }, modebar: { bgcolor: 'rgba(255, 255, 255, 0)', From 880321d73ecedfbe13e0f2af4a011ea8cfe56f1a Mon Sep 17 00:00:00 2001 From: Yanay1 Date: Sun, 15 Nov 2020 13:19:26 -0800 Subject: [PATCH 05/62] sig overflow --- inst/html_output/Results.html | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/inst/html_output/Results.html b/inst/html_output/Results.html index 4f7aaac4..3c9d90d4 100644 --- a/inst/html_output/Results.html +++ b/inst/html_output/Results.html @@ -107,7 +107,7 @@
-
+
From 570e03898a52a308fdf1802c3c77c6b576e1f50c Mon Sep 17 00:00:00 2001 From: Yanay1 Date: Tue, 8 Dec 2020 19:47:36 -0800 Subject: [PATCH 06/62] layout for no dend changes --- inst/html_output/Results.html | 8 ++++---- inst/html_output/src/upper_left_content.js | 9 +++++++++ 2 files changed, 13 insertions(+), 4 deletions(-) diff --git a/inst/html_output/Results.html b/inst/html_output/Results.html index 3c9d90d4..0c1f4038 100644 --- a/inst/html_output/Results.html +++ b/inst/html_output/Results.html @@ -66,7 +66,7 @@
-
+
-
+
@@ -282,7 +282,7 @@
-
+
@@ -327,7 +327,7 @@
-
+
-<<<<<<< HEAD
-======= -
->>>>>>> 9defe27e2f74721941497b9d0be25c114f076251
From e79f768620218b28e88a9b264d7f38eff7f6f07e Mon Sep 17 00:00:00 2001 From: Yanay1 Date: Wed, 20 Jan 2021 12:03:26 -0800 Subject: [PATCH 08/62] modules fix --- R/methods-Module.R | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/R/methods-Module.R b/R/methods-Module.R index 18fa01f4..fe4b21fa 100644 --- a/R/methods-Module.R +++ b/R/methods-Module.R @@ -1,5 +1,3 @@ - - calcHotspotModules <- function(object, model="normal", tree=FALSE, genes=1000, num_umi=NULL, min_gene_threshold=20, n_neighbors=NULL, fdr_threshold=0.05) { @@ -74,7 +72,7 @@ calcHotspotModules <- function(object, model="normal", tree=FALSE, genes=1000, } } - colnames(hs_module_scores) <- names(modules) + colnames(hs_module_scores) <- sort(names(modules)) object@modData <- modules if (length(object@sigData) > 0) { From 756584d79a480b9b05f2e959998c83155cd77d8f Mon Sep 17 00:00:00 2001 From: Yanay1 Date: Wed, 20 Jan 2021 12:14:49 -0800 Subject: [PATCH 09/62] merged changes --- R/methods-Module.R | 6 ------ 1 file changed, 6 deletions(-) diff --git a/R/methods-Module.R b/R/methods-Module.R index fe54ad20..0cb80e48 100644 --- a/R/methods-Module.R +++ b/R/methods-Module.R @@ -1,10 +1,4 @@ -<<<<<<< HEAD -calcHotspotModules <- function(object, model="normal", tree=FALSE, genes=1000, -======= - - calcHotspotModules <- function(object, model="normal", tree=FALSE, number_top_genes=1000, ->>>>>>> 97f7568d065586ab6894478faf43ad6c0c342058 num_umi=NULL, min_gene_threshold=20, n_neighbors=NULL, fdr_threshold=0.05) { From 6a7061b1e207cc9b84c992a132f7e4534b122282 Mon Sep 17 00:00:00 2001 From: Yanay1 Date: Tue, 26 Jan 2021 13:56:25 -0800 Subject: [PATCH 10/62] small layout changes --- R/methods-Module.R | 74 ++++++++++++++++++---- R/methods-Vision.R | 1 - inst/html_output/Results.html | 4 +- inst/html_output/src/PhyloPlotly.js | 5 +- inst/html_output/src/lower_left_content.js | 1 - inst/html_output/src/main.js | 1 - inst/html_output/src/upper_left_content.js | 15 +++-- 7 files changed, 74 insertions(+), 27 deletions(-) diff --git a/R/methods-Module.R b/R/methods-Module.R index 0cb80e48..f16936f0 100644 --- a/R/methods-Module.R +++ b/R/methods-Module.R @@ -1,6 +1,29 @@ -calcHotspotModules <- function(object, model="normal", tree=FALSE, number_top_genes=1000, - num_umi=NULL, min_gene_threshold=20, n_neighbors=NULL, - fdr_threshold=0.05) { +#' Initializes a new VISION object. +#' +#' +#' @param object Vision Object +#' @param model model argument for Hotspot, one of \itemize{ +#' \item normal +#' \item danb +#' \item bernoulli +#' \item none +#' } +#' @param tree whether to use tree as latent space. If TRUE, object should have +#' a tree slot. +#' @param number_top_genes hotspot argument for number of genes to consider +#' @param num_umi optional dataframe containing umi counts in first column for +#' barcodes +#' @param min_gene_threshold minimum number of genes in hotspot module +#' @param n_neighbors number of neighbors to consider in latent space +#' @param fdr_threshold threshold for significance +#' +#' Populates the modData, HotspotModuleScores, ModuleSignatureEnrichment +#' and HotspotObject slots of object, as well as recalculates signature scores +#' for new modules. +calcHotspotModules <- function(object, model="normal", tree=FALSE, + number_top_genes=1000,num_umi=NULL, + min_gene_threshold=20, n_neighbors=NULL, + fdr_threshold=0.05) { hotspot <- import("hotspot", convert=F) @@ -13,7 +36,7 @@ calcHotspotModules <- function(object, model="normal", tree=FALSE, number_top_ge gene_subset = object@params$latentSpace$projectionGenes - if (is.null(gene_subset)) { + if (is.na(gene_subset)) { gene_subset <- applyFilters(exprData, object@params$latentSpace$projectionGenesMethod, object@params$latentSpace$threshold, 2) @@ -25,7 +48,7 @@ calcHotspotModules <- function(object, model="normal", tree=FALSE, number_top_ge sds = apply(exprData, 1, sd) exprData = exprData[which(sds > 0), ] - # TODO add UMI support + # generate the Hotspot object in python, potentially using the tree if (tree) { message("Using Tree") ete3 <- import("ete3", convert=F) @@ -49,22 +72,25 @@ calcHotspotModules <- function(object, model="normal", tree=FALSE, number_top_ge } } + # create knn graph, specify nn or use object default if (is.null(n_neighbors)) { hs$create_knn_graph(F, n_neighbors = as.integer(object@params$numNeighbors)) } else { hs$create_knn_graph(F, n_neighbors = as.integer(n_neighbors)) } + # perform hotspot analysis and store results in R hs_results <- hs$compute_autocorrelations(jobs=as.integer(workers)) hs_genes <- hs_results$loc[hs_results$FDR$le(fdr_threshold)]$sort_values('Z', ascending=F)$head(as.integer(number_top_genes))$index hs$compute_local_correlations(hs_genes, jobs=as.integer(workers)) - hs$create_modules(min_gene_threshold=as.integer(min_gene_threshold)) + hs$create_modules(min_gene_threshold=as.integer(min_gene_threshold), fdr_threshold=fdr_threshold) hs_module_scores <- py_to_r(hs$calculate_module_scores()) hs_modules <- py_to_r(hs$modules) modules <- list() + # add the modules with name scheme HOTSPOT_{TREE if using TREE}_# for (i in unique(c(hs_modules))) { if (i !=-1) { names <- dimnames(hs_modules[hs_modules == i])[[1]] @@ -80,6 +106,7 @@ calcHotspotModules <- function(object, model="normal", tree=FALSE, number_top_ge } } + # store module scores colnames(hs_module_scores) <- sort(names(modules)) object@modData <- modules @@ -98,16 +125,13 @@ calcHotspotModules <- function(object, model="normal", tree=FALSE, number_top_ge object@Hotspot <- list(hs) object@ModuleHotspotScores <- hs_module_scores object <- analyzeLocalCorrelationsModules(object, tree) - - - return(object) } -#' calculate module scores +#' Calculate module scores (signature scores but on the modules) #' #' For each module-cell pair, compute a score that captures the level of #' correspondence between the cell and the module. @@ -185,6 +209,7 @@ calcModuleScores <- function( #' consistency of the resulting space with the signature scores is computed #' to find signals that are captured successfully by the projections. #' @param object the VISION object +#' @param tree whether to use the tree object as latent space for neighbors #' @return the VISION object with values set for the analysis results #' @export analyzeLocalCorrelationsModules <- function(object, tree=FALSE) { @@ -228,12 +253,18 @@ analyzeLocalCorrelationsModules <- function(object, tree=FALSE) { return(object) } + +#' Computes the hypergeometric overlap test for modules and signatures +#' @param object the vision object. +#' @return list(statistic values, p values, clusters of signatures) +#' calc_mod_sig_enrichment <- function(object) { modules <- object@modData original_signatures <- object@sigData signatures <- list() sig_names <- list() for (signature in original_signatures) { + # calculate enrichment for both the up signal and down signal signature genes directional <- all(c(1, -1) %in% signature@sigDict) if (directional) { up <- names(which(signature@sigDict == 1)) @@ -255,6 +286,7 @@ calc_mod_sig_enrichment <- function(object) { genes <- rownames(object@exprData) + # calculate the enrichments stats <- c() p_values <- c() for (signature in signatures) { @@ -282,13 +314,21 @@ calc_mod_sig_enrichment <- function(object) { colnames(p_values) <- mod_names rownames(p_values) <- sig_names + # group the signatures assignments <- group_modules_enrichment(stats, p_values) return(list("statistics"=stats, "p_vals"=p_values, "cl"=assignments)) } - +#' Calculate the hypergeometric enrichment for two sets from a population +#' +#' @param set1 +#' @param set2 +#' @param genes the population +#' @return c(statistic, p value) +#' Statisic = log (observed overlap / expected overlap) +#' P value = 1- hypergeometric(observed overlap -1, max(|set1|, |set2|), |genes| - |set1|, min(|set1|, |set2|)) calc_set_enrichment <- function(set1, set2, genes) { N <- length(genes) m <- max(length(set1), length(set2)) @@ -307,7 +347,11 @@ calc_set_enrichment <- function(set1, set2, genes) { return(c(stat, p_value)) } - +#' Make the clusters for the modules by enrichment. +#' For now we just assign each signature to each cluster, could filter to only include once. +#' +#' @param stats +#' @param pvals group_modules_enrichment <- function(stats, pvals) { sigs <- rownames(stats) mods <- colnames(stats) @@ -319,6 +363,10 @@ group_modules_enrichment <- function(stats, pvals) { } +#' Generates signature objects for the overlap sets between modules and signatures +#' @param object the vision object +#' +#' Populates the modData slot with overlap signatures. generateOverlapSignatures <- function(object) { message("Generating Module Signature Overlaps...\n") sigs <- rownames(object@ModuleSignatureEnrichment$statistics) @@ -428,7 +476,5 @@ clusterModScores <- function(object, variables = "All") { object@ClusterComparisons[["Modules"]] <- out return(object) - } - diff --git a/R/methods-Vision.R b/R/methods-Vision.R index 9082dd60..a19350f3 100644 --- a/R/methods-Vision.R +++ b/R/methods-Vision.R @@ -267,7 +267,6 @@ setMethod("Vision", signature(data = "matrixORSparse"), .Object@params$latentSpace$projectionGenesMethod <- projection_genes .Object@params$latentSpace$projectionGenes <- NA } else { - print("Here") .Object@params$latentSpace$projectionGenesMethod <- NA .Object@params$latentSpace$projectionGenes <- vapply( projection_genes, toupper, "", USE.NAMES = FALSE) diff --git a/inst/html_output/Results.html b/inst/html_output/Results.html index 0c1f4038..70aaf1af 100644 --- a/inst/html_output/Results.html +++ b/inst/html_output/Results.html @@ -107,7 +107,7 @@
-
+
@@ -294,7 +294,7 @@
From 664a89ec8454d91b3d3a6f8d86c12e10aef361e5 Mon Sep 17 00:00:00 2001 From: Matthew Jones Date: Tue, 9 Mar 2021 13:05:57 -0800 Subject: [PATCH 19/62] updated some imports; removed mandatory upper case gene names --- NAMESPACE | 4 ++++ R/methods-Signature.R | 2 -- R/methods-Vision.R | 5 +---- 3 files changed, 5 insertions(+), 6 deletions(-) diff --git a/NAMESPACE b/NAMESPACE index 3eddf38e..4d71be67 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -1,6 +1,7 @@ # Generated by roxygen2: do not edit by hand export(Vision) +export(PhyloVision) export(addSignatures) export(addTSNE) export(addUMAP) @@ -10,6 +11,7 @@ export(annotateLatentComponents) export(applyMicroClustering) export(calcModuleScores) export(calcSignatureScores) +export(calcHotspotModules) export(clusterSigScores) export(computeLatentSpace) export(convertGeneIds) @@ -33,9 +35,11 @@ exportMethods(getSelections) exportMethods(getSignatureAutocorrelation) exportMethods(getSignatureDifferential) exportMethods(getSignatureScores) +exportMethods(phyloAnalyze) exportMethods(saveAndViewResults) exportMethods(viewResults) import(Matrix) +import(dplyr) import(Rcpp) import(ape) import(loe) diff --git a/R/methods-Signature.R b/R/methods-Signature.R index 6943c4a5..309270c3 100644 --- a/R/methods-Signature.R +++ b/R/methods-Signature.R @@ -61,8 +61,6 @@ Signature <- function(sigDict, name, source, metaData="") { stop("Missing source file.") } - names(sigDict) <- toupper(names(sigDict)) - .Object <- new("Signature", sigDict = sigDict, name = name, source = source, metaData = metaData) diff --git a/R/methods-Vision.R b/R/methods-Vision.R index a19350f3..a7a74e16 100644 --- a/R/methods-Vision.R +++ b/R/methods-Vision.R @@ -107,7 +107,6 @@ setMethod("Vision", signature(data = "matrixORSparse"), .Object@params$signatures <- list() .Object@params$micropooling <- list() - rownames(data) <- toupper(rownames(data)) toRemove <- rownames(data)[duplicated(rownames(data))] if (length(toRemove) > 0){ message(sprintf( @@ -139,7 +138,6 @@ setMethod("Vision", signature(data = "matrixORSparse"), } # unnormalizedData might have more genes than exprData # and it might have more cells than exprData - rownames(unnormalizedData) <- toupper(rownames(unnormalizedData)) HAS_CORRECT_CELLS <- length(setdiff( colnames(.Object@exprData), colnames(unnormalizedData) @@ -268,8 +266,7 @@ setMethod("Vision", signature(data = "matrixORSparse"), .Object@params$latentSpace$projectionGenes <- NA } else { .Object@params$latentSpace$projectionGenesMethod <- NA - .Object@params$latentSpace$projectionGenes <- vapply( - projection_genes, toupper, "", USE.NAMES = FALSE) + .Object@params$latentSpace$projectionGenes <- projection_genes .Object@params$latentSpace$projectionGenes = intersect(rownames(.Object@exprData), .Object@params$latentSpace$projectionGenes) } From a15430286823640c8795899b8073c82c7de75517 Mon Sep 17 00:00:00 2001 From: Yanay1 Date: Wed, 24 Mar 2021 16:27:22 -0700 Subject: [PATCH 20/62] code clean up and trying new tree cluster --- R/Microclusters.R | 102 ++++++++--- R/Projections.R | 14 +- R/Utilities.R | 130 +++++++++++--- R/methods-Module.R | 269 ++++++++++++++++++---------- R/methods-Vision.R | 2 +- inst/html_output/src/PhyloPlotly.js | 3 +- 6 files changed, 369 insertions(+), 151 deletions(-) diff --git a/R/Microclusters.R b/R/Microclusters.R index 8c82bb11..ba15801e 100644 --- a/R/Microclusters.R +++ b/R/Microclusters.R @@ -326,6 +326,7 @@ readjust_clusters <- function(clusters, data, cellsPerPartition=100) { return(clusters) } + #' Pools columns of a numeric matrix #' #' Uses the provided pools to merge columns of the supplied data matrix @@ -383,6 +384,7 @@ poolMatrixRows <- function(data, pools) { return(pooled_data) } + #' create "super-cells" by pooling together single cells #' @param expr expression data (genes x cells matrix) #' @param pools cluster association of each cell @@ -424,7 +426,9 @@ poolMatrixCols_Inner <- function(expr, pools) { #' @param reach number of clusters to attempt to generate #' @return List of clusters, each entry being a vector of indices representing #' samples in the cluster. -treeCluster <- function(tree, reach=10) { +#' +#' @export +treeCluster1 <- function(tree, reach=10) { high <- length(tree$tip.label) low <- 0 while (T) { @@ -470,13 +474,15 @@ treeCluster <- function(tree, reach=10) { } -#' Performs a breadth first search to create a specific number of clusters -#' Clusters are split based on depth +#' Performs a breadth first search to create a specific number of clusters. +#' Clusters are split based on depth. #' #' @param tree object of class phylo #' @param reach number of clusters to attempt to generate #' @return List of clusters, each entry being a vector of indices representing #' samples in the cluster. +#' +#' @export treeCluster2 <- function(tree, reach=10) { if (reach > length(tree$tip.label)) { stop("Number of clusters is too high.") @@ -557,35 +563,91 @@ treeCluster3 <- function(tree, reach=10) { } while (length(cl) > reach) { - cs <- c() - for (c in cl) { - cs <- append(cs, length(c)) - } - - smallest_i <- which.min(cs) - tip1 <- which(tree$tip.label == cl[[smallest_i]][1]) - dists <- c() - for (i in 1:length(cl)) { - tip2 <- which(tree$tip.label == cl[[i]][1]) - dists <- append(dists, trivial_dist(tree, tip1, tip2)) - } + cs <- c() + for (c in cl) { + cs <- append(cs, length(c)) + } + + smallest_i <- which.min(cs) + tip1 <- which(tree$tip.label == cl[[smallest_i]][1]) + dists <- c() + for (i in 1:length(cl)) { + tip2 <- which(tree$tip.label == cl[[i]][1]) + dists <- append(dists, trivial_dist(tree, tip1, tip2)) + } + + dists[smallest_i] <- dists[smallest_i] + max(dists) + closest_cluster_i <- which.min(dists) + cl[[min(c(closest_cluster_i, smallest_i))]] <- append(cl[[smallest_i]], cl[[closest_cluster_i]]) + cl[[max(c(closest_cluster_i, smallest_i))]] <- NULL + } + + return(cl) +} + +#' Bottom up tree clustering approach +#' Merge the smallest cluster and the cluster next to it in the plotly tree. +#' Plotly tree is sorted by ultrametric depth +#' +#' @param tree object of class phylo +#' @param reach number of clusters to attempt to generate +#' @return List of clusters, each entry being a vector of tips representing +#' samples in the cluster. +treeCluster4 <- function(tree, reach=10) { + if (reach > length(tree$tip.label)) { + stop("Number of clusters is too high.") + } + + node_depths <- node.depth(tree, method = 2) + root <- find_root(tree) + # PQ + cluster_parents <- c() + for (node in tree$tip.label) { + cluster_parents[[node]] <- 1 + } + + # BFS on internal nodes, with pq ordered by the maximum clade size we would get splitting on that node + while (T) { + cluster_parents <- cluster_parents[order(unlist(cluster_parents), decreasing = F)] # sorted by decreasing size + remove <- as.integer(names(cluster_parents)[1]) # smallest cluster + cluster_parents <- cluster_parents[-1] # after removing + + + removed_parent <- get_parent(tree, ) + + children <- get_children(tree, remove) + for (child in children) { + cluster_parents[[as.name(child)]] <- get_min_cluster_size(tree, child) - dists[smallest_i] <- dists[smallest_i] + max(dists) - closest_cluster_i <- which.min(dists) - cl[[min(c(closest_cluster_i, smallest_i))]] <- append(cl[[smallest_i]], cl[[closest_cluster_i]]) - cl[[max(c(closest_cluster_i, smallest_i))]] <- NULL + } + + # Don't make too many clusters + if (length(cluster_parents) >= reach) { + break + } } + # Map the internal nodes from PQ to clusters (their children) + cl <- list() + for (cluster in seq_len(length(cluster_parents))) { + cellId <- as.integer(names(cluster_parents)[cluster]) + + all_children <- get_all_children(tree, cellId) %>% (function(x) {return(tree$tip.label[x])}) + cl[[cluster]] <- all_children + } + return(cl) } -#' Generate clusters for a tree of minimum size (unless children of root) +#' Generate clade-clusters for a tree of minimum size (unless children of root) #' #' @param tree object of class phylo #' @param minSize minimum clade size for a clade to be expanded #' @return List of clusters, each entry being a vector of tips representing +#' WARNING: This won't work well for tree's with broad multifurcations +#' @export treeClusterMinCladeSize <- function(tree, minSize=30) { nodeLabels <- tree$node.label numC <- length(tree$tip.label) diff --git a/R/Projections.R b/R/Projections.R index 14b3316a..25bf053a 100644 --- a/R/Projections.R +++ b/R/Projections.R @@ -378,20 +378,28 @@ setMethod("computeKNNWeights", signature(object = "matrix"), ) -#' compute for each vector the weights to apply to it's K nearest neighbors +#' Compute for each vector the weights to apply to it's K nearest neighbors +#' #' @importFrom Matrix rowSums #' @importFrom Matrix sparseMatrix #' @importFrom matrixStats rowMaxs #' @param object tree to use for KNN #' @param K Number of neighbors to consider. +#' @param lcaKNN whether to use LCA based KNN (cluster by minimum size) +#' WARNING: lcaKNN doesn't perform well with broad multifurcations #' @return a list of two items: #' indices: matrix, cells X neighbors #' Each row specifies indices of nearest neighbors #' weights: matrix, cells X neighbors #' Corresponding weights to nearest neighbors setMethod("computeKNNWeights", signature(object = "phylo"), - function(object, K = round(sqrt(length(object$tip.label)))) { - k <- find_knn_parallel_tree(object, K) + function(object, K = round(sqrt(length(object$tip.label))), lcaKNN=FALSE, minSize=20) { + if (lcaKNN) { + k <- lcaBasedTreeKNN(object, minSize = minSize) + } else { + k <- find_knn_parallel_tree(object, K) + } + nn <- k[[1]] d <- k[[2]] diff --git a/R/Utilities.R b/R/Utilities.R index ec57920b..c7eb65cf 100644 --- a/R/Utilities.R +++ b/R/Utilities.R @@ -806,7 +806,6 @@ knn_tree <- function(leaves, k, distances) { } - #' Parallel KNN for Trees #' #' Computes nearest-neighbor indices and distances @@ -852,6 +851,47 @@ find_knn_parallel_tree <- function(tree, K) { return(list(index=idx, dist=dists)) } + + +#' Add custom tree based neighbor and weights to a hotspot object +#' +#' @param tree object of class phylo +#' @param the hotspot object to add the nw to +#' @param minSize the minimum number of neighbors of the node +#' @return the hotspot object +lcaBasedTreeKNN <- function(tree, minSize=20) { + tips <- tree$tip.label + nTips <- length(tips) + neighbors <- data.frame(t(matrix(seq_len(nTips), ncol = nTips, nrow= nTips))) + rownames(neighbors) <- tips + + + weights <- data.frame(matrix(0, ncol = nTips, nrow= nTips)) + for (tip in seq_len(nTips)) { + my_neighbors <- minSizeCladeNeighbors(tree, tip, minSize) + + weights[tip, my_neighbors] <- 1 + } + + neighbors_no_diag <- data.frame(matrix(ncol = nTips -1, nrow= nTips)) + weights_no_diag <- data.frame(matrix(ncol = nTips -1, nrow= nTips)) + + for (tip in seq_len(nTips)) { + neighbors_no_diag[tip, ] <- neighbors[tip, -tip] + weights_no_diag[tip, ] <- weights[tip, -tip] + } + + rownames(neighbors_no_diag) <- tips + rownames(weights_no_diag) <- tips + + colnames(neighbors_no_diag) <- seq_len(nTips-1) - 1 + colnames(weights_no_diag) <- seq_len(nTips-1) - 1 + return(list("neighbors"=as.matrix(neighbors_no_diag), "weights"=as.matrix(weights_no_diag))) +} + + + + #' Generate an ultrametric tree #' #' @param tree an object of class phylo @@ -1012,38 +1052,74 @@ get_min_cluster_size <- function(tree, node) { #' Trivial distance function for arbitrary tree clustering #' -#' Trivial distance is defined as the difference in depths between the +#' Number of mutations along path from tip1 to LCA(tip1, tip2) +#' Ensures if on same clade, join. #' #' @param tree an object of class phylo #' @param tip1 the first leaf #' @param tip2 the second leaf #' @return the trivial distance between tip1, tip2 +#' +#' @export trivial_dist <- function(tree, tip1, tip2) { - depths <- node.depth(tree) - edges <- tree$edge - path1 <- c(tip1) - root <- find_root(tree) - parent <- tip1 - while (T) { - parent <- edges[, 1][edges[, 2] == parent] - path1 <- append(path1, parent) - if (parent == root) { - break - } + # node depths of tree + edges <- tree$edge + # Get the path from tip1 to root + path1 <- c(tip1) + root <- find_root(tree) + parent <- tip1 + while (T) { + parent <- edges[, 1][edges[, 2] == parent] + path1 <- append(path1, parent) + if (parent == root) { + break } - - path2 <- c(tip2) - parent <- tip2 - while (T) { - parent <- edges[, 1][edges[, 2] == parent] - path2 <- append(path2, parent) - if (parent == root || parent %in% path1) { - break - } + } + + mrca <- getMRCA(tree, c(tip1, tip2)) # MRCA of both + + + # Depths of the internal nodes that represent the parents of tip1, tip2 right before LCA + # ie the 'diverging' point or first split + path_length <- which(path1 == mrca) + + # Return the absolute difference between the depths + return(path_length) +} + + + + + +#' Depth of tip1 parent immediately after LCA(tip1, tip2) +#' +#' @param tree an object of class phylo +#' @param tip1 the first leaf +#' @param tip2 the second leaf +#' @return the trivial distance between tip1, tip2 +#' +#' @export +lca_based_depth <- function(tree, tip1, tip2) { + depths <- node.depth(tree) + edges <- tree$edge + # Get the path from tip1 to root + path1 <- c(tip1) + root <- find_root(tree) + parent <- tip1 + while (T) { + parent <- edges[, 1][edges[, 2] == parent] + path1 <- append(path1, parent) + if (parent == root) { + break } - - tip1_depth_prev <- depths[path1[which(path1 == path2[length(path2)]) - 1]] - tip2_depth_prev <- depths[path2[length(path2)] - 1] - - return(abs(tip1_depth_prev - tip2_depth_prev)) + } + + mrca <- getMRCA(tree, c(tip1, tip2)) # MRCA of both + + # Depths of the internal nodes that represent the parents of tip1, tip2 right before LCA + # ie the 'diverging' point or first split + lca_child_depth <- depths[path1[which(path1 == mrca) - 1]] + + # Return the absolute difference between the depths + return(lca_child_depth) } \ No newline at end of file diff --git a/R/methods-Module.R b/R/methods-Module.R index 37d5f6d6..f5982dfb 100644 --- a/R/methods-Module.R +++ b/R/methods-Module.R @@ -1,5 +1,4 @@ -#' Initializes a new VISION object. -#' +#' Perform Hotspot analysis on Vision Object #' #' @param object Vision Object #' @param model model argument for Hotspot, one of \itemize{ @@ -10,127 +9,183 @@ #' } #' @param tree whether to use tree as latent space. If TRUE, object should have #' a tree slot. -#' @param number_top_genes hotspot argument for number of genes to consider +#' @param number_top_genes Hotspot argument for number of genes to consider #' @param num_umi optional dataframe containing umi counts in first column for #' barcodes -#' @param min_gene_threshold minimum number of genes in hotspot module +#' @param min_gene_threshold minimum number of genes in Hotspot module #' @param n_neighbors number of neighbors to consider in latent space #' @param autocorrelation_fdr threshold for significance for genes autocorr #' @param clustering_fdr threshold for significance for clustering modules +#' @param nn_precomp precomputed neighbors, barcodes x neighbors +#' @param wt_precomp precomputed weights, barcodes x neighbors #' #' Populates the modData, HotspotModuleScores, ModuleSignatureEnrichment #' and HotspotObject slots of object, as well as recalculates signature scores #' for new modules. -calcHotspotModules <- function(object, model="normal", tree=FALSE, - number_top_genes=1000,num_umi=NULL, +#' @return the modified Vision object +#' +#' @export +hsAnalyze <- function(object, model="normal", tree=FALSE, + number_top_genes=1000, num_umi=NULL, min_gene_threshold=20, n_neighbors=NULL, autocorrelation_fdr=0.05, clustering_fdr=0.5, nn_precomp=NULL, wt_precomp=NULL) { - hotspot <- import("hotspot", convert=F) + # Init Hotspot + hs <- hsInit(object, model, tree, num_umi) + # Init Hotspot KNN + hs <- hsCreateKnnGraph(hs, object, n_neighbors=NULL, nn_precomp=NULL, wt_precomp=NULL) + # perform Hotspot analysis and store results in R + hs_genes <- hsComputeAutoCorrelations(hs, number_top_genes=1000, autocorrelation_fdr=0.05) + # Compute localcorr + hs <- hsComputeLocalCorrelations(hs, hs_genes) + # Calculate Hotspot Module Scores for informative genes + hs <- hsCalculateModuleScores(hs, min_gene_threshold, clustering_fdr) + # Cluster Hotspot modules and perform Vision based analysis on HS Modules and + object <- analyzeHotspotObjectVision(object, hs, tree) - workers <- getOption("mc.cores") - if (is.null(workers)){ - workers <- 1 - } - if (model == "danb") { - # Don't take the log if danb - exprData = object@exprData - } else { - # take the log2 otherwise - exprData = matLog2(object@exprData) - } - - gene_subset = object@params$latentSpace$projectionGenes - - if (is.na(gene_subset)) { - gene_subset <- applyFilters(exprData, - object@params$latentSpace$projectionGenesMethod, - object@params$latentSpace$threshold, 2) - } - - exprData = as.data.frame(as.matrix(exprData)[gene_subset,]) + return(object) +} - # remove genes that do not have any standard deviation - sds = apply(exprData, 1, sd) - exprData = exprData[which(sds > 0), ] - # generate the Hotspot object in python, potentially using the tree - if (tree) { - message("Using Tree") - ete3 <- import("ete3", convert=F) - nwk <- write.tree(object@tree) - pyTree <- ete3$Tree(nwk, format = 8L) - if (is.null(num_umi)) { - hs <- hotspot$Hotspot(exprData, tree=pyTree, model=model) - } else { - py$umi_df <- r_to_py(num_umi) - py_run_string("umi_counts = umi_df.iloc[:, 0]") - hs <- hotspot$Hotspot(exprData, tree=pyTree, model=model, umi_counts=py$umi_counts) - } - +#' Init Hotspot object from Vision Object +#' +#' @param object the Vision Object +#' @param model the model for Hotspot (ie "normal", "danb"...) +#' @param tree boolean, whether to use the tree as ls +#' @param num_umi df of barcodes x num_umi +#' @return the Hotspot object +#' +#' @export +hsInit <- function(object, model="normal", tree=F, num_umi=NULL) { + hotspot <- import("hotspot", convert=F) + + workers <- getOption("mc.cores") + if (is.null(workers)){ + workers <- 1 + } + if (model == "danb") { + # Don't take the log if danb + exprData = object@exprData + } else { + # take the log2 otherwise + exprData = matLog2(object@exprData) + } + + gene_subset = object@params$latentSpace$projectionGenes + + if (is.na(gene_subset)) { + gene_subset <- applyFilters(exprData, + object@params$latentSpace$projectionGenesMethod, + object@params$latentSpace$threshold, 2) + } + + exprData = as.data.frame(as.matrix(exprData)[gene_subset,]) + + # remove genes that do not have any standard deviation + sds = apply(exprData, 1, sd) + exprData = exprData[which(sds > 0), ] + + # generate the Hotspot object in python, potentially using the tree + if (tree) { + message("Using Tree") + ete3 <- import("ete3", convert=F) + nwk <- write.tree(object@tree) + pyTree <- ete3$Tree(nwk, format = 8L) + if (is.null(num_umi)) { + hs <- hotspot$Hotspot(exprData, tree=pyTree, model=model) } else { - if (is.null(num_umi)) { - hs <- hotspot$Hotspot(exprData, latent=as.data.frame(object@LatentSpace), model=model) - } else { - py$umi_df <- r_to_py(num_umi) - py_run_string("umi_counts = umi_df.iloc[:, 0]") - hs <- hotspot$Hotspot(exprData, latent=as.data.frame(object@LatentSpace), model=model, umi_counts=py$umi_counts) - } + py$umi_df <- r_to_py(num_umi) + py_run_string("umi_counts = umi_df.iloc[:, 0]") + hs <- hotspot$Hotspot(exprData, tree=pyTree, model=model, umi_counts=py$umi_counts) } - # create knn graph, specify nn or use object default - if (!is.null(nn_precomp)) { - hs$neighbors <- nn_precomp - hs$weights <- wt_precomp - } else if (is.null(n_neighbors)) { - hs$create_knn_graph(F, n_neighbors = as.integer(object@params$numNeighbors)) + } else { + if (is.null(num_umi)) { + hs <- hotspot$Hotspot(exprData, latent=as.data.frame(object@LatentSpace), model=model) } else { - hs$create_knn_graph(F, n_neighbors = as.integer(n_neighbors)) + py$umi_df <- r_to_py(num_umi) + py_run_string("umi_counts = umi_df.iloc[:, 0]") + hs <- hotspot$Hotspot(exprData, latent=as.data.frame(object@LatentSpace), model=model, umi_counts=py$umi_counts) } + } - # perform hotspot analysis and store results in R - hs_results <- hs$compute_autocorrelations(jobs=as.integer(workers)) - hs_genes <- hs_results$loc[hs_results$FDR$le(autocorrelation_fdr)]$sort_values('Z', ascending=F)$head(as.integer(number_top_genes))$index - - hs <- hsComputeLocalCorrelations(hs, hs_genes, workers) - - hs <- createHotspotModulesCalcScores(hs, min_gene_threshold, clustering_fdr) - - object <- analyzeHotspotObject(object, hs, tree) - - return(object) + return(hs) +} + + +#' Init KNN graph in Hotspot object +#' +#' @param nn_precomp precomputed neighbors, barcodes x neighbors +#' @param wt_precomp precomputed weights, barcodes x neighbors +#' @return the Hotspot object with KNN initialized +#' +#' @export +hsCreateKnnGraph <- function(hs, object, n_neighbors=NULL, nn_precomp=NULL, wt_precomp=NULL) { + # create knn graph, specify nn or use object default + if (!is.null(nn_precomp)) { + hs$neighbors <- nn_precomp + hs$weights <- wt_precomp + } else if (is.null(n_neighbors)) { + hs$create_knn_graph(F, n_neighbors = as.integer(object@params$numNeighbors)) + } else { + hs$create_knn_graph(F, n_neighbors = as.integer(n_neighbors)) + } + return(hs) } +#' Compute Hotspot auto correlations +#' +#' @param hs the Hotspot object +#' @param number_top_genes Hotspot argument for number of genes to consider +#' @param autocorrelation_fdr threshold for significance for genes autocorr +#' @return list of HS genes +#' +#' @export +hsComputeAutoCorrelations <- function(hs, number_top_genes=1000, autocorrelation_fdr=0.05) { + workers <- getOption("mc.cores") + if (is.null(workers)){ + workers <- 1 + } + + hs_results <- hs$compute_autocorrelations(jobs=as.integer(workers)) + hs_genes <- hs_results$loc[hs_results$FDR$le(autocorrelation_fdr)]$sort_values('Z', ascending=F)$head(as.integer(number_top_genes))$index + return(hs_genes) +} + -#' Interface function to compute local correlations for hotspot +#' Interface function to compute local correlations for Hotspot #' Warning: modifies the hs argument -#' @param hs the hotspot object -#' @param hs_genes hotspot genes -#' @param workers num core +#' @param hs the Hotspot object +#' @param hs_genes Hotspot genes #' @return the populated hs object #' #' @export -hsComputeLocalCorrelations <- function(hs, hs_genes, workers) { - hs$compute_local_correlations(hs_genes, jobs=as.integer(workers)) - return(hs) +hsComputeLocalCorrelations <- function(hs, hs_genes) { + workers <- getOption("mc.cores") + if (is.null(workers)){ + workers <- 1 + } + hs$compute_local_correlations(hs_genes, jobs=as.integer(workers)) + return(hs) } -#' Analyze a hotspot object using built in methods such +#' Analyze a Hotspot object using built in methods such #' such as local correlation, signature overlap, etc. -#' Necessary to run this function for hotpot functionality in viewer to work. +#' Necessary to run this function for Hotspot functionality in viewer to work. #' #' @param object the VISION object -#' @param hs the hotspot python object loaded by reticulate -#' @param tree whether to use tree as latent space. If TRUE, object should have +#' @param hs the Hotspot python object loaded by Reticulate +#' @param tree whether to use tree as latent space. If TRUE, object should have a tree #' #' @return the modified VISION object with the following slots filled: #' Populates the modData, HotspotModuleScores, ModuleSignatureEnrichment #' and HotspotObject slots of object, as well as recalculates signature scores #' for new modules. +#' #' @export -analyzeHotspotObject <- function(object, hs, tree=FALSE) { +analyzeHotspotObjectVision <- function(object, hs, tree=FALSE) { hs_module_scores <- hs$module_scores hs_modules <- hs$modules @@ -182,7 +237,7 @@ analyzeHotspotObject <- function(object, hs, tree=FALSE) { object@ModuleHotspotScores <- hs_module_scores object <- analyzeLocalCorrelationsModules(object, tree) - # save the hotspot object + # save the Hotspot object object <- addHotspotToVision(object, hs) return(object) @@ -191,13 +246,14 @@ analyzeHotspotObject <- function(object, hs, tree=FALSE) { #' Create Hotspot Modules and calculate module scores given a HS object #' with local correlations already calculated -#' @param hs the hotspot object, must have ran compute_local_correlations already +#' +#' @param hs the Hotspot object, must have ran compute_local_correlations already #' @param min_gene_threshold min genes per module #' @param clustering_fdr p value for clustering genes #' @return the modified hs object #' #' @export -createHotspotModulesCalcScores <- function(hs, min_gene_threshold=20, clustering_fdr=0.5, plot=F) { +hsCalculateModuleScores <- function(hs, min_gene_threshold=20, clustering_fdr=0.5, plot=F) { hs$create_modules(min_gene_threshold=as.integer(min_gene_threshold), fdr_threshold=clustering_fdr) hs$calculate_module_scores() @@ -210,13 +266,14 @@ createHotspotModulesCalcScores <- function(hs, min_gene_threshold=20, clustering #' Add HS python obj to vision OBJECT +#' #' @param object Vision object #' @param hs python hs object -#' @return vision object +#' @return Vision object with hs populated #' #' @export addHotspotToVision <- function(object, hs) { - # save the hotspot object + # save the Hotspot object pickle <- import("pickle", convert=F) py$hs <- hs py$pickle <- pickle @@ -242,6 +299,7 @@ addHotspotToVision <- function(object, hs) { #' the overall signature score. Default = TRUE. This is used for inspecting #' genes in a signature in the output report #' @return the VISION object, with the @ModScores and @ModGeneImportance slots populated +#' #' @export calcModuleScores <- function( object, mod_norm_method = NULL, mod_gene_importance = TRUE) { @@ -303,9 +361,11 @@ calcModuleScores <- function( #' different projection onto low-dimensional space are computed, and the #' consistency of the resulting space with the signature scores is computed #' to find signals that are captured successfully by the projections. +#' #' @param object the VISION object #' @param tree whether to use the tree object as latent space for neighbors #' @return the VISION object with values set for the analysis results +#' #' @export analyzeLocalCorrelationsModules <- function(object, tree=FALSE) { @@ -350,10 +410,12 @@ analyzeLocalCorrelationsModules <- function(object, tree=FALSE) { #' Computes the hypergeometric overlap test for modules and signatures -#' @param object the vision object. +#' +#' @param object the Vision object. #' @param skip_down whether to ignore down signatures in overlap #' @return list(statistic values, p values, clusters of signatures) #' +#' @export calc_mod_sig_enrichment <- function(object, skip_down=TRUE) { modules <- object@modData original_signatures <- object@sigData @@ -425,13 +487,15 @@ calc_mod_sig_enrichment <- function(object, skip_down=TRUE) { #' Calculate the hypergeometric enrichment for two sets from a population +#' Statisic = log (observed overlap / expected overlap) +#' P value = 1- hypergeometric(observed overlap -1, max(|set1|, |set2|), |genes| - |set1|, min(|set1|, |set2|)) #' #' @param set1 #' @param set2 #' @param genes the population #' @return c(statistic, p value) -#' Statisic = log (observed overlap / expected overlap) -#' P value = 1- hypergeometric(observed overlap -1, max(|set1|, |set2|), |genes| - |set1|, min(|set1|, |set2|)) +#' +#' @export calc_set_enrichment <- function(set1, set2, genes) { N <- length(genes) m <- max(length(set1), length(set2)) @@ -450,11 +514,16 @@ calc_set_enrichment <- function(set1, set2, genes) { return(c(stat, p_value)) } + #' Make the clusters for the modules by enrichment. -#' For now we just assign each signature to each cluster, could filter to only include once. +#' For now we just assign each signature to each cluster, could filter to only include once, +#' so that each one appears in the modules x sigs table. #' -#' @param stats -#' @param pvals +#' @param stats overlap stats from calc_set_enrichment +#' @param pvals overlap p values from calc_set_enrichment +#' @return assignments of each signature to each module +#' +#' @export group_modules_enrichment <- function(stats, pvals) { sigs <- rownames(stats) mods <- colnames(stats) @@ -467,9 +536,10 @@ group_modules_enrichment <- function(stats, pvals) { #' Generates signature objects for the overlap sets between modules and signatures -#' @param object the vision object +#' @param object the Vision object +#' @return Vision Object, populates the modData slot with overlap signatures. #' -#' Populates the modData slot with overlap signatures. +#' @export generateOverlapSignatures <- function(object) { message("Generating Module Signature Overlaps...\n") sigs <- rownames(object@ModuleSignatureEnrichment$statistics) @@ -505,6 +575,7 @@ generateOverlapSignatures <- function(object) { #' @param object the VISION object #' @param variables which columns of the meta-data to use for comparisons #' @return the VISION object with the @ClusterComparisons modules slot populated +#' #' @export clusterModScores <- function(object, variables = "All") { @@ -616,12 +687,14 @@ saveHSBytestToPickle <- function(path, bytes) { } -#' Add custom tree based neighbor and weights to a hotspot object +#' Add custom tree based neighbor and weights to a Hotspot object #' #' @param tree object of class phylo -#' @param the hotspot object to add the nw to +#' @param the Hotspot object to add the nw to #' @param minSize the minimum number of neighbors of the node -#' @return the hotspot object +#' @return the Hotspot object +#' +#' @export lcaBasedHotspotNeighbors <- function(tree, hotspot, minSize=20) { tips <- tree$tip.label nTips <- length(tips) diff --git a/R/methods-Vision.R b/R/methods-Vision.R index a7a74e16..2755af8f 100644 --- a/R/methods-Vision.R +++ b/R/methods-Vision.R @@ -722,7 +722,7 @@ setMethod("analyze", signature(object="Vision"), if (hotspot) { message("Hotspot Analysis") - object <- calcHotspotModules(object, model="danb", tree) + object <- hsAnalyze(object, model="danb", tree) } diff --git a/inst/html_output/src/PhyloPlotly.js b/inst/html_output/src/PhyloPlotly.js index 3cb41b43..ac64ac95 100644 --- a/inst/html_output/src/PhyloPlotly.js +++ b/inst/html_output/src/PhyloPlotly.js @@ -343,7 +343,7 @@ PhyloPlotly.prototype.setLinearCoords = function() { if (!isTip(tree)) { // internal node var childrenHeights = []; - tree["branchset"].forEach(function(child) { + tree["branchset"].sort(function(a, b) {return a["depth"] - b["depth"]}).forEach(function(child) { setLinearCoord(child); childrenHeights.push(child["y"]) }); @@ -405,7 +405,6 @@ PhyloPlotly.prototype.selectedLinesTrace = function(nodes){ hoverinfo: 'skip' } - console.log(horizontalLines) return (horizontalLines) } From 40d718f57e865c2b79cba5cedf7178b57a124bee Mon Sep 17 00:00:00 2001 From: Yanay1 Date: Tue, 30 Mar 2021 13:36:08 -0700 Subject: [PATCH 21/62] code clean up and trying new tree cluster --- R/AnalysisFunctions.R | 2 +- R/Microclusters.R | 66 ++++--------------------------------------- R/Projections.R | 2 +- 3 files changed, 8 insertions(+), 62 deletions(-) diff --git a/R/AnalysisFunctions.R b/R/AnalysisFunctions.R index d272dee9..bc8a7a67 100644 --- a/R/AnalysisFunctions.R +++ b/R/AnalysisFunctions.R @@ -18,7 +18,7 @@ clusterCells <- function(object, tree=FALSE) { } else { message("Using Tree to compute clusters...\n") # Get the MRCA matrix and convert the node indexes to depths - cl <- treeCluster3(object@tree) + cl <- maxSizeCladewiseTreeCluster(object@tree) } names(cl) <- paste('Cluster', seq(length(cl))) diff --git a/R/Microclusters.R b/R/Microclusters.R index ba15801e..a142fd44 100644 --- a/R/Microclusters.R +++ b/R/Microclusters.R @@ -420,7 +420,7 @@ poolMatrixCols_Inner <- function(expr, pools) { #' Performs a binary search on a depth d such that -#' if depth(u, v) <= d then u and v are in the same cluster +#' if depth(LCA(u, v)) <= d then u and v are in the same cluster #' #' @param tree object of class phylo #' @param reach number of clusters to attempt to generate @@ -428,7 +428,7 @@ poolMatrixCols_Inner <- function(expr, pools) { #' samples in the cluster. #' #' @export -treeCluster1 <- function(tree, reach=10) { +depthBasedTreeCluster <- function(tree, reach=10) { high <- length(tree$tip.label) low <- 0 while (T) { @@ -483,7 +483,7 @@ treeCluster1 <- function(tree, reach=10) { #' samples in the cluster. #' #' @export -treeCluster2 <- function(tree, reach=10) { +depthBasedCladewiseTreeCluster <- function(tree, reach=10) { if (reach > length(tree$tip.label)) { stop("Number of clusters is too high.") } @@ -522,13 +522,13 @@ treeCluster2 <- function(tree, reach=10) { #' Performs a breadth first search to create a specific number of clusters -#' Clusters are split to prioritize cluster size +#' Clusters are split to prioritize max cluster size #' #' @param tree object of class phylo #' @param reach number of clusters to attempt to generate #' @return List of clusters, each entry being a vector of tips representing #' samples in the cluster. -treeCluster3 <- function(tree, reach=10) { +maxSizeCladewiseTreeCluster <- function(tree, reach=10) { if (reach > length(tree$tip.label)) { stop("Number of clusters is too high.") } @@ -585,63 +585,9 @@ treeCluster3 <- function(tree, reach=10) { return(cl) } -#' Bottom up tree clustering approach -#' Merge the smallest cluster and the cluster next to it in the plotly tree. -#' Plotly tree is sorted by ultrametric depth -#' -#' @param tree object of class phylo -#' @param reach number of clusters to attempt to generate -#' @return List of clusters, each entry being a vector of tips representing -#' samples in the cluster. -treeCluster4 <- function(tree, reach=10) { - if (reach > length(tree$tip.label)) { - stop("Number of clusters is too high.") - } - - node_depths <- node.depth(tree, method = 2) - root <- find_root(tree) - # PQ - cluster_parents <- c() - for (node in tree$tip.label) { - cluster_parents[[node]] <- 1 - } - - # BFS on internal nodes, with pq ordered by the maximum clade size we would get splitting on that node - while (T) { - cluster_parents <- cluster_parents[order(unlist(cluster_parents), decreasing = F)] # sorted by decreasing size - remove <- as.integer(names(cluster_parents)[1]) # smallest cluster - cluster_parents <- cluster_parents[-1] # after removing - - - removed_parent <- get_parent(tree, ) - - children <- get_children(tree, remove) - for (child in children) { - cluster_parents[[as.name(child)]] <- get_min_cluster_size(tree, child) - - } - - # Don't make too many clusters - if (length(cluster_parents) >= reach) { - break - } - } - - # Map the internal nodes from PQ to clusters (their children) - cl <- list() - for (cluster in seq_len(length(cluster_parents))) { - cellId <- as.integer(names(cluster_parents)[cluster]) - - all_children <- get_all_children(tree, cellId) %>% (function(x) {return(tree$tip.label[x])}) - cl[[cluster]] <- all_children - } - - return(cl) -} - - #' Generate clade-clusters for a tree of minimum size (unless children of root) +#' #' #' @param tree object of class phylo #' @param minSize minimum clade size for a clade to be expanded diff --git a/R/Projections.R b/R/Projections.R index 25bf053a..43f8e525 100644 --- a/R/Projections.R +++ b/R/Projections.R @@ -385,7 +385,7 @@ setMethod("computeKNNWeights", signature(object = "matrix"), #' @importFrom matrixStats rowMaxs #' @param object tree to use for KNN #' @param K Number of neighbors to consider. -#' @param lcaKNN whether to use LCA based KNN (cluster by minimum size) +#' @param lcaKNN whether to use LCA based KNN (cluster by minimum size), if false defaults to cophenetic distance (random tie breaking). #' WARNING: lcaKNN doesn't perform well with broad multifurcations #' @return a list of two items: #' indices: matrix, cells X neighbors From 161b1b043e641c0501430110864b9c5fbe3682f2 Mon Sep 17 00:00:00 2001 From: Yanay1 Date: Tue, 30 Mar 2021 13:38:45 -0700 Subject: [PATCH 22/62] code clean up and trying new tree cluster --- R/methods-Module.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/methods-Module.R b/R/methods-Module.R index f5982dfb..8665e88f 100644 --- a/R/methods-Module.R +++ b/R/methods-Module.R @@ -35,7 +35,7 @@ hsAnalyze <- function(object, model="normal", tree=FALSE, # Init Hotspot KNN hs <- hsCreateKnnGraph(hs, object, n_neighbors=NULL, nn_precomp=NULL, wt_precomp=NULL) # perform Hotspot analysis and store results in R - hs_genes <- hsComputeAutoCorrelations(hs, number_top_genes=1000, autocorrelation_fdr=0.05) + hs_genes <- hsComputeAutoCorrelations(hs, number_top_genes=number_top_genes, autocorrelation_fdr=autocorrelation_fdr) # Compute localcorr hs <- hsComputeLocalCorrelations(hs, hs_genes) # Calculate Hotspot Module Scores for informative genes From 682c1d305fcf617a9d201be0ea77b3d2af2d92c3 Mon Sep 17 00:00:00 2001 From: Yanay1 Date: Tue, 30 Mar 2021 13:40:03 -0700 Subject: [PATCH 23/62] code clean up and trying new tree cluster --- R/methods-Module.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/methods-Module.R b/R/methods-Module.R index 8665e88f..ca7c5530 100644 --- a/R/methods-Module.R +++ b/R/methods-Module.R @@ -33,7 +33,7 @@ hsAnalyze <- function(object, model="normal", tree=FALSE, # Init Hotspot hs <- hsInit(object, model, tree, num_umi) # Init Hotspot KNN - hs <- hsCreateKnnGraph(hs, object, n_neighbors=NULL, nn_precomp=NULL, wt_precomp=NULL) + hs <- hsCreateKnnGraph(hs, object, n_neighbors=n_neighbors, nn_precomp=nn_precomp, wt_precomp=wt_precomp) # perform Hotspot analysis and store results in R hs_genes <- hsComputeAutoCorrelations(hs, number_top_genes=number_top_genes, autocorrelation_fdr=autocorrelation_fdr) # Compute localcorr From 59828bffbaf51110c8bb9422f0e4e985adf1ff1f Mon Sep 17 00:00:00 2001 From: Yanay1 Date: Wed, 31 Mar 2021 16:14:27 -0700 Subject: [PATCH 24/62] code clean up and trying new tree cluster --- R/Microclusters.R | 24 ++++++++++++------------ R/methods-Module.R | 17 +++++------------ R/methods-Vision.R | 2 +- 3 files changed, 18 insertions(+), 25 deletions(-) diff --git a/R/Microclusters.R b/R/Microclusters.R index a142fd44..f21ce7cd 100644 --- a/R/Microclusters.R +++ b/R/Microclusters.R @@ -423,12 +423,12 @@ poolMatrixCols_Inner <- function(expr, pools) { #' if depth(LCA(u, v)) <= d then u and v are in the same cluster #' #' @param tree object of class phylo -#' @param reach number of clusters to attempt to generate +#' @param target number of clusters to attempt to generate #' @return List of clusters, each entry being a vector of indices representing #' samples in the cluster. #' #' @export -depthBasedTreeCluster <- function(tree, reach=10) { +depthBasedTreeCluster <- function(tree, target=10) { high <- length(tree$tip.label) low <- 0 while (T) { @@ -457,12 +457,12 @@ depthBasedTreeCluster <- function(tree, reach=10) { } } - if (num_clusters >= reach) { + if (num_clusters >= target) { if(low == d) { break } low <- d - } else if (num_clusters < reach) { + } else if (num_clusters < target) { if(high == d) { break } @@ -478,13 +478,13 @@ depthBasedTreeCluster <- function(tree, reach=10) { #' Clusters are split based on depth. #' #' @param tree object of class phylo -#' @param reach number of clusters to attempt to generate +#' @param target number of clusters to attempt to generate #' @return List of clusters, each entry being a vector of indices representing #' samples in the cluster. #' #' @export -depthBasedCladewiseTreeCluster <- function(tree, reach=10) { - if (reach > length(tree$tip.label)) { +depthBasedCladewiseTreeCluster <- function(tree, target=10) { + if (target > length(tree$tip.label)) { stop("Number of clusters is too high.") } @@ -504,7 +504,7 @@ depthBasedCladewiseTreeCluster <- function(tree, reach=10) { cluster_parents[[as.name(child)]] <- node_depths[child] } - if (length(cluster_parents) >= reach) { + if (length(cluster_parents) >= target) { break } } @@ -525,11 +525,11 @@ depthBasedCladewiseTreeCluster <- function(tree, reach=10) { #' Clusters are split to prioritize max cluster size #' #' @param tree object of class phylo -#' @param reach number of clusters to attempt to generate +#' @param target number of clusters to attempt to generate #' @return List of clusters, each entry being a vector of tips representing #' samples in the cluster. -maxSizeCladewiseTreeCluster <- function(tree, reach=10) { - if (reach > length(tree$tip.label)) { +maxSizeCladewiseTreeCluster <- function(tree, target=10) { + if (target > length(tree$tip.label)) { stop("Number of clusters is too high.") } @@ -562,7 +562,7 @@ maxSizeCladewiseTreeCluster <- function(tree, reach=10) { cl[[cluster]] <- all_children } - while (length(cl) > reach) { + while (length(cl) > target) { cs <- c() for (c in cl) { cs <- append(cs, length(c)) diff --git a/R/methods-Module.R b/R/methods-Module.R index ca7c5530..ee4afb41 100644 --- a/R/methods-Module.R +++ b/R/methods-Module.R @@ -16,8 +16,6 @@ #' @param n_neighbors number of neighbors to consider in latent space #' @param autocorrelation_fdr threshold for significance for genes autocorr #' @param clustering_fdr threshold for significance for clustering modules -#' @param nn_precomp precomputed neighbors, barcodes x neighbors -#' @param wt_precomp precomputed weights, barcodes x neighbors #' #' Populates the modData, HotspotModuleScores, ModuleSignatureEnrichment #' and HotspotObject slots of object, as well as recalculates signature scores @@ -25,15 +23,15 @@ #' @return the modified Vision object #' #' @export -hsAnalyze <- function(object, model="normal", tree=FALSE, +runHotspot <- function(object, model="normal", tree=FALSE, number_top_genes=1000, num_umi=NULL, min_gene_threshold=20, n_neighbors=NULL, - autocorrelation_fdr=0.05, clustering_fdr=0.5, nn_precomp=NULL, wt_precomp=NULL) { + autocorrelation_fdr=0.05, clustering_fdr=0.5) { # Init Hotspot hs <- hsInit(object, model, tree, num_umi) # Init Hotspot KNN - hs <- hsCreateKnnGraph(hs, object, n_neighbors=n_neighbors, nn_precomp=nn_precomp, wt_precomp=wt_precomp) + hs <- hsCreateKnnGraph(hs, object, n_neighbors=n_neighbors) # perform Hotspot analysis and store results in R hs_genes <- hsComputeAutoCorrelations(hs, number_top_genes=number_top_genes, autocorrelation_fdr=autocorrelation_fdr) # Compute localcorr @@ -115,17 +113,12 @@ hsInit <- function(object, model="normal", tree=F, num_umi=NULL) { #' Init KNN graph in Hotspot object #' -#' @param nn_precomp precomputed neighbors, barcodes x neighbors -#' @param wt_precomp precomputed weights, barcodes x neighbors #' @return the Hotspot object with KNN initialized #' #' @export -hsCreateKnnGraph <- function(hs, object, n_neighbors=NULL, nn_precomp=NULL, wt_precomp=NULL) { +hsCreateKnnGraph <- function(hs, object, n_neighbors=NULL) { # create knn graph, specify nn or use object default - if (!is.null(nn_precomp)) { - hs$neighbors <- nn_precomp - hs$weights <- wt_precomp - } else if (is.null(n_neighbors)) { + if (is.null(n_neighbors)) { hs$create_knn_graph(F, n_neighbors = as.integer(object@params$numNeighbors)) } else { hs$create_knn_graph(F, n_neighbors = as.integer(n_neighbors)) diff --git a/R/methods-Vision.R b/R/methods-Vision.R index 2755af8f..ad11870d 100644 --- a/R/methods-Vision.R +++ b/R/methods-Vision.R @@ -722,7 +722,7 @@ setMethod("analyze", signature(object="Vision"), if (hotspot) { message("Hotspot Analysis") - object <- hsAnalyze(object, model="danb", tree) + object <- runHotspot(object, model="danb", tree) } From 37fbca0270c61c2e0f2ef06143dfedbbf7ad282a Mon Sep 17 00:00:00 2001 From: Yanay1 Date: Thu, 1 Apr 2021 16:21:35 -0700 Subject: [PATCH 25/62] code clean up and trying new tree cluster --- R/Microclusters.R | 1 - 1 file changed, 1 deletion(-) diff --git a/R/Microclusters.R b/R/Microclusters.R index f21ce7cd..f7d0870e 100644 --- a/R/Microclusters.R +++ b/R/Microclusters.R @@ -533,7 +533,6 @@ maxSizeCladewiseTreeCluster <- function(tree, target=10) { stop("Number of clusters is too high.") } - # node_depths <- node.depth(tree) root <- find_root(tree) cluster_parents <- c() cluster_parents[[as.name(root)]] <- get_max_cluster_size(tree, root) From ef8814edf3f926085785918761e05bfc28d7d3dd Mon Sep 17 00:00:00 2001 From: Yanay1 Date: Wed, 7 Apr 2021 13:59:13 -0700 Subject: [PATCH 26/62] Added vignettes --- vignettes/metastasisPhyloVision.Rmd | 77 ++++++++++++++++++++++++++++ vignettes/phlyoVision.Rmd | 79 +++++++++++++++++++++++++++++ vignettes/spatialHotspot.Rmd | 48 ++++++++++++++++++ 3 files changed, 204 insertions(+) create mode 100644 vignettes/metastasisPhyloVision.Rmd create mode 100644 vignettes/phlyoVision.Rmd create mode 100644 vignettes/spatialHotspot.Rmd diff --git a/vignettes/metastasisPhyloVision.Rmd b/vignettes/metastasisPhyloVision.Rmd new file mode 100644 index 00000000..fa1fee5d --- /dev/null +++ b/vignettes/metastasisPhyloVision.Rmd @@ -0,0 +1,77 @@ +--- +title: "metastasis" +output: html_document +--- + +```{r setup, include=FALSE} +knitr::opts_chunk$set(echo = TRUE) +devtools::load_all("/home/eecs/yanayrosen/VISION/") # change to just load VISION +library(ape) +library(reticulate) +``` + +## R Markdown + +This is an R Markdown document. Markdown is a simple formatting syntax for authoring HTML, PDF, and MS Word documents. For more details on using R Markdown see . + +When you click the **Knit** button a document will be generated that includes both content as well as the output of any embedded R code chunks within the document. You can embed an R code chunk like this: + +## Creating a Phylo Vision Object with a Tree + +Vision objects now support dendrograms for visualization and analysis. To create the Phylo-VISION object, you need all of the same data, an expression matrix, and metadata and/or signatures, but you also include a tree object from the Ape package. +```{r create} +# Read the expression and meta data +expr <- read_10x(expression = "/data/yosef2/users/mattjones/projects/PhyloVision/data/metastasis_data/GRCh38/matrix.mtx", + genes = "/data/yosef2/users/mattjones/projects/PhyloVision/data/metastasis_data/GRCh38/genes.tsv", + barcodes = "/data/yosef2/users/mattjones/projects/PhyloVision/data/metastasis_data/GRCh38/barcodes.tsv") + + +barcodes <- read.table("/data/yosef2/users/mattjones/projects/PhyloVision/data/metastasis_data/GRCh38/barcodes.tsv", check.names = FALSE, sep="\t") +latent <- read.table("/data/yosef2/users/mattjones/projects/PhyloVision/data/metastasis_data/latent.csv", check.names=FALSE, sep="\t", row.names = 1, header=TRUE) +row.names(latent) <- barcodes[, 1] + +meta <- read.table("/data/yosef2/users/mattjones/projects/PhyloVision/data/metastasis_data/GSM4905335_meta.5k.tsv.gz", check.names = FALSE, sep = "\t", row.names = 1, header=TRUE) +# meta$Cell_Type <- as.factor(meta$Cell_Type) +# Signature file +sigs = c("c5.go.bp.v7.2.symbols.gmt", "h.all.v5.2.symbols.gmt", "c4.cgn.v7.2.symbols.gmt") + +# Read the trees +lg7_tree <- read.tree("/data/yosef2/users/mattjones/projects/PhyloVision/data/metastasis_data/lg7_tree_hybrid_priors.alleleThresh.processed.txt") +lg4_tree <- read.tree("/data/yosef2/users/mattjones/projects/PhyloVision/data/metastasis_data/lg4_tree_hybrid_priors.alleleThresh.processed.txt") + +# Subset trees with expression +lg7_barcodes <- intersect(lg7_tree$tip.label, colnames(expr)) +lg4_barcodes <- intersect(lg4_tree$tip.label, colnames(expr)) + +lg7_tree <- keep.tip(lg7_tree, lg7_barcodes) +lg4_tree <- keep.tip(lg4_tree, lg4_barcodes) + +# Collapse one mutations +lg7_tree <- collapse.singles(lg7_tree) +lg4_tree <- collapse.singles(lg4_tree) + +expr_lg7 <- expr[, lg7_barcodes] +expr_lg4 <- expr[, lg4_barcodes] + +latent_lg7 <- latent[lg7_barcodes,] +latent_lg4 <- latent[lg4_barcodes,] + +meta_lg7 <- meta[lg7_barcodes,] +meta_lg4 <- meta[lg4_barcodes,] + +# Construct the Vision object +vis_lg7 <- PhyloVision(tree=lg7_tree, data=expr_lg7, latentSpace=latent_lg7, signatures=sigs, meta=meta_lg7, num_neighbors=40, projection_genes="threshold", sig_gene_threshold=0.05, projection_methods=c("tSNE30", "tSNE10", "UMAP")) +vis_lg4 <- PhyloVision(tree=lg4_tree, data=expr_lg4, latentSpace=latent_lg4, signatures=sigs, meta=meta_lg4, num_neighbors=40, projection_genes="threshold", sig_gene_threshold=0.05, projection_methods=c("tSNE30", "tSNE10", "UMAP")) +``` +Next, we can perform the normal Vision analysis using the tree as the latent space. + +```{r analyze} +vis_lg7 <- phyloAnalyze(vis_lg7) +vis_lg4 <- phyloAnalyze(vis_lg4) +``` + +We can also perform Hotspot module analysis. +```{r hotspot} +vis_lg7 <- runHotspot(vis_lg7, model="danb", tree=TRUE, min_gene_threshold=120, n_neighbors = 40, clustering_fdr = 1.0) +vis_lg4 <- runHotspot(vis_lg4, model="danb", tree=TRUE, min_gene_threshold=120, n_neighbors = 40, clustering_fdr = 1.0) +``` \ No newline at end of file diff --git a/vignettes/phlyoVision.Rmd b/vignettes/phlyoVision.Rmd new file mode 100644 index 00000000..efc1d812 --- /dev/null +++ b/vignettes/phlyoVision.Rmd @@ -0,0 +1,79 @@ +--- +title: "VisCas Vignette" +author: "Yanay Rosen" +date: "9/30/2020" +output: html_document +--- + +```{r setup, include=FALSE} +knitr::opts_chunk$set(echo = TRUE) +devtools::load_all("~/Desktop/VISION/") # change to just load VISION +library(ape) +library(reticulate) +``` + +## Creating a Phylo Vision Object with a Tree + +Vision objects now support dendrograms for visualization and analysis. To create the Phylo-VISION object, you need all of the same data, an expression matrix, and metadata and/or signatures, but you also include a tree object from the Ape package. +```{r create} +# Read the expression and meta data +expr <- read.table("VisCasVignetteFiles/expr.tsv", check.names = FALSE, sep = "\t") +umap <- read.table("VisCasVignetteFiles/umap_data.csv", check.names=FALSE, sep=",", row.names = 1, header=TRUE) +meta <- read.table("VisCasVignetteFiles/meta.tsv", check.names = FALSE, sep = "\t", row.names = 1, header=TRUE) +meta$Cell_Type <- as.factor(meta$Cell_Type) +# Signature file +sigs = c("signatures/h.all.v5.2.symbols.gmt", "signatures/c6.all.v7.2.symbols.gmt", "signatures/c8.all.v7.2.symbols.gmt") + +# Read the tree +tree <- read.tree("VisCasVignetteFiles/tree") +# Collapse one mutations +tree <- collapse.singles(tree) +expr <- expr[, tree$tip.label] + +# Construct the Vision object +vis <- PhyloVision(tree=tree, data=expr, latentSpace=umap, signatures=sigs, meta=meta, num_neighbors=30) +``` + +Next, we can perform the normal Vision analysis using the tree as the latent space. + +``` {r analyze} +vis <- phyloAnalyze(vis) +``` +We can also perform Hotspot module analysis. +```{r hotspot} +vis <- runHotspot(vis, model="normal", tree=TRUE, min_gene_threshold=50, n_neighbors = 30, number_top_genes = 12438) +``` +The full Hotspot API is exposed for analysis as well: +```{r eval=FALSE} +# Init Hotspot +hs <- hsInit(vis, model = "normal", tree=TRUE) +# Init Hotspot KNN +hs <- hsCreateKnnGraph(hs, vis, n_neighbors=30) +# perform Hotspot analysis and store results in R +hs_genes <- hsComputeAutoCorrelations(hs, number_top_genes=12438) +# Compute localcorr +hs <- hsComputeLocalCorrelations(hs, hs_genes) +# Calculate Hotspot Module Scores for informative genes +hs <- hsCalculateModuleScores(hs) +# Cluster Hotspot modules and perform Vision based analysis on HS Modules and +vis <- analyzeHotspotObjectVision(vis, hs, tree=TRUE) +``` + + + +Finally, we can launch the Vision browser. +```{r eval=FALSE} +viewResults(vis) +``` + +```{r inspectModules} +hs <- loadHotspotObject(bytes=vis@Hotspot[[1]]) +library(reticulate) +use_python('/usr/bin/python3') +``` +```{python modulesPlot} +import matplotlib.pyplot as plt +import hotspot +hs.plot_local_correlations() +plt.show() +``` diff --git a/vignettes/spatialHotspot.Rmd b/vignettes/spatialHotspot.Rmd new file mode 100644 index 00000000..16228832 --- /dev/null +++ b/vignettes/spatialHotspot.Rmd @@ -0,0 +1,48 @@ +--- +title: "Vision Hotspot Vignette" +author: "Yanay Rosen" +date: "9/30/2020" +output: html_document +--- + +```{r setup, include=FALSE} +knitr::opts_chunk$set(echo = TRUE) +devtools::load_all("~/Desktop/VISION/") # change to just load VISION +library(reticulate) +``` + +## Creating a Vision Object + +First, we create a Vision object +```{r create} +# Read the expression and meta data +expr <- read.table("VisHotspotVignetteFiles/expr.tsv", check.names = FALSE, sep = "\t") +meta <- read.table("VisHotspotVignetteFiles/meta.tsv", check.names = FALSE, sep = "\t", row.names = 1, header=TRUE) + +# Signature file +sig = "VisHotspotVignetteFiles/h.all.v5.2.symbols.gmt" + +# Read and create the coordinates +pos <- read.table("VisHotspotVignetteFiles/BeadLocationsForR.csv", sep=",", check.names = FALSE, row.names=1, header=TRUE) +pos["X"] <- pos$ycoord +pos["Y"] <- -1 * pos$xcoord +pos <- pos[c("X", "Y")] + +# Construct the Vision object +vis <- Vision(expr, signatures=c(sig), latentSpace = pos, meta=meta) # TODO add relevant signatures +``` + +Next, we can perform the normal Vision analysis using the tree as the latent space. We need to tell Vision to use the Tree as the latent space and to calculate neighbors. + +``` {r analyze} +vis <- analyze(vis) +``` +We can also perform Hotspot module analysis. +```{r hotspot} +vis <- runHotspot(vis, model="bernoulli", num_umi=meta["num_umi"]) +``` + +Finally, we can launch the Vision browser. +```{r view} +viewResults(vis) +``` From a1427c36065dc8151847f0e4f117a3a0c71c7f1c Mon Sep 17 00:00:00 2001 From: Yanay1 Date: Wed, 28 Apr 2021 12:17:04 -0700 Subject: [PATCH 27/62] updating vignettes --- vignettes/phlyoVision.Rmd | 19 +++++++++++-------- vignettes/spatialHotspot.Rmd | 2 +- 2 files changed, 12 insertions(+), 9 deletions(-) diff --git a/vignettes/phlyoVision.Rmd b/vignettes/phlyoVision.Rmd index efc1d812..f2c6e28f 100644 --- a/vignettes/phlyoVision.Rmd +++ b/vignettes/phlyoVision.Rmd @@ -43,7 +43,8 @@ We can also perform Hotspot module analysis. ```{r hotspot} vis <- runHotspot(vis, model="normal", tree=TRUE, min_gene_threshold=50, n_neighbors = 30, number_top_genes = 12438) ``` -The full Hotspot API is exposed for analysis as well: + +The full Hotspot API is exposed for analysis as well. For more on the Hotspot API see [here](https://yoseflab.github.io/Hotspot/index.html) ```{r eval=FALSE} # Init Hotspot hs <- hsInit(vis, model = "normal", tree=TRUE) @@ -59,13 +60,7 @@ hs <- hsCalculateModuleScores(hs) vis <- analyzeHotspotObjectVision(vis, hs, tree=TRUE) ``` - - -Finally, we can launch the Vision browser. -```{r eval=FALSE} -viewResults(vis) -``` - +We can also access further Hotspot functionality using Reticulate and Python. ```{r inspectModules} hs <- loadHotspotObject(bytes=vis@Hotspot[[1]]) library(reticulate) @@ -77,3 +72,11 @@ import hotspot hs.plot_local_correlations() plt.show() ``` + + +Finally, we can launch the Vision browser. +```{r eval=FALSE} +viewResults(vis) +``` + + diff --git a/vignettes/spatialHotspot.Rmd b/vignettes/spatialHotspot.Rmd index 16228832..a0c819bd 100644 --- a/vignettes/spatialHotspot.Rmd +++ b/vignettes/spatialHotspot.Rmd @@ -32,7 +32,7 @@ pos <- pos[c("X", "Y")] vis <- Vision(expr, signatures=c(sig), latentSpace = pos, meta=meta) # TODO add relevant signatures ``` -Next, we can perform the normal Vision analysis using the tree as the latent space. We need to tell Vision to use the Tree as the latent space and to calculate neighbors. +Next, we can perform the normal Vision analysis using the spatial coordinates as the latent space. ``` {r analyze} vis <- analyze(vis) From ac1f1fe3cbbdaa4f0c1d9ae4727a573e9a6e938d Mon Sep 17 00:00:00 2001 From: David DeTomaso Date: Sun, 18 Apr 2021 18:47:06 -0700 Subject: [PATCH 28/62] Adding server API documentation --- API.md | 502 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 502 insertions(+) create mode 100644 API.md diff --git a/API.md b/API.md new file mode 100644 index 00000000..dd843774 --- /dev/null +++ b/API.md @@ -0,0 +1,502 @@ +# GET: /SessionInfo +Returns high-level configuration info on this VISION session. Mostly used +to enable/disable features in the visualizer. + +- 'name': A title for this session (shown in the top title bar) +- 'meta\_sigs': Names of meta-data signatures. Sent here as a convenience as +numeric meta-data signatures and gene signatures get combined in the display +and often lookups are needed to distinguish. +- 'ncells': Total number of cells +- 'pooled': Whether or not there is micro-pooling +- 'has\_sigs': Whether or not there are gene signatures +- 'has\_proteins': Whether or not there are CITE-seq proteins +- 'has\_lca': Whether or not LC Annotator analysis is available +- 'has\_tree': Whether or not Trajectories are available + +Response structure: +``` + { + 'name': 'Session Name', + 'meta_sigs': [list of string], + 'ncells': int, + 'pooled': bool, + 'has_sigs': bool, + 'has_proteins': bool, + 'has_lca': bool, + 'has_tree': bool, + } +``` + +# GET: /Signature/Scores/ +Return the per-cell signature scores for signature: `` +Data comes from obj@SigScores matrix + +Response structure: + +``` + { + 'cells': [list of str, cell ids...], + 'values': [list of Number, per cell signature scores], + } +``` + +# GET: /Signature/Meta/ +Return the per-cell meta-data values for variable: `` +Data comes from obj@metaData dataframe + +Response structure: + +``` + { + 'cells': [list of str, cell ids...], + 'values': [list of Number or string, per-cell meta-data values], + } +``` + +# GET: /Signature/Info/ +Returns information associated with a signature +Data comes from object@sigData + +Response structure: + +``` + { + 'sigDict': { # signature-gene weights + 'GeneName1': 1, + 'GeneName2': -1, + ... + }, + 'name': 'Signature Name', + 'source': 'Signature source', # typically filename where signature was loaded from + 'metaData': 'Signature description...', # second column in .gmt file + 'geneImportance': { # signature-gene importance values + 'GeneName1': .1, + 'GeneName2': .01, + ... + } + } +``` + +# GET: /Signature/Expression// +Returns expression values for `` grouped by ``. +This is used to generate the gene x cluster heatmap in the bottom left +Values are computed on the fly at the server + +Response structure +``` +{ + 'data': list of list of Number (2d matrix, outer index is row index) + 'sample_labels': column labels for the matrix in 'data' + 'gene_labels': row labels for the matrix in 'data' +} +``` + +# GET: /Proteins/\/Values +Returns the per-cell protein expression values for `` +Data comes from obj@proteinData matrix + +Response structure: +``` + { + 'cells': [list of str, cell ids...], + 'values': [list of Number, per cell protein expression], + } +``` + +# GET: /FilterGroup/SigClusters/Normal +For each signature, describes the assignment of signatures to signature-clusters +This is used to group signatures in the upper-left section + +Response structure: +``` +{ + "Signature Name" (str): (int), + ... +} +``` + +# GET: /FilterGroup/SigClusters/Proteins +For each protein, describes the assignment of proteins to protein-clusters +Proteins aren't actually clustered in the interface. Every protein is assigned to cluster #1 + +Response structure: +``` +{ + "Protein Name" (str): 1, + ... +} +``` + +# GET: /FilterGroup/SigClusters/Meta +For each meta-data variable, describes the assignment of each variable to meta-data clusters +This is used when micropools are created to group factor variables with their expanded +percent-value-per-micropool representations + +Response structure: +``` +{ + "Metadata variable Name" (str): (int), + ... +} +``` + +# GET: /Projections//coordinates/ +Returns the coordinates for projection `` in column `` +Since the scatter plot can show more than just projects, this has been expanded to also +return coordinates from the latent space or other meta-data variables. `` can +come from names in object@Projections, or can be "Meta Data" to refer to object@metaData or +"Latent Space" to refer to object@LatentSpace. In either case `` should refer +to an associated column. + +Response structure: + +List of list of `[coordinate, 'cell id']` + +``` +[ + [coordinate (float): 'cell id' (str)], + [coordinate (float): 'cell id' (str)], + [coordinate (float): 'cell id' (str)], + ... +[ +``` + +# GET: /Projections/list +Returns information on projections and other variables that can be plotted in the main +scatter-plot panel. Used to create the dropdown menus. + +Response structure: + +Dictionary where keys are the name of projections/meta data/latent space and the values are +a list of the associated columns + +``` +{ + 'projection_name_1': list of column names in the projection, + 'projection_name_2': list of column names in the projection, + 'Meta Data': list of numeric meta-data variables, + 'Latent Space': list of column names in the latent space +} +``` + +# GET: /PearsonCorr/Normal +Gets information for the LC Annotator - the correlation of each signature with each latent component + +Response structure: +``` +{ + "zscores": list of list of correlation coefficients (N signatures x N components), + "pvals": list of list of p-values (N signatures x N components), + "proj_labels": list of latent space column names in the same order as columns of 'zscores'/'pvals', + "sig_labels": list of signature names in the same order as columns of 'zscores'/'pvals', +} +``` + +# GET: /PearsonCorr/Proteins +Gets information for the LC Annotator - the correlation of each protein with each latent component + +Response structure: +``` +{ + "zscores": list of list of correlation coefficients (N proteins x N components), + "pvals": list of list of p-values (N proteins x N components), + "proj_labels": list of latent space column names in the same order as columns of 'zscores'/'pvals', + "sig_labels": list of proteins names in the same order as columns of 'zscores'/'pvals', +} +``` + +# GET: /PearsonCorr/Meta +Gets information for the LC Annotator - the correlation of each numeric meta-data variable with each latent component + +Response structure: +``` +{ + "zscores": list of list of correlation coefficients (N variables x N components), + "pvals": list of list of p-values (N variables x N components), + "proj_labels": list of latent space column names in the same order as columns of 'zscores'/'pvals', + "sig_labels": list of variables names in the same order as columns of 'zscores'/'pvals', +} +``` + +# POST: /DE +Requests a differential expression analysis from the server. + +Determines the set of cells used for the numerator (i.e. _num or _n) and for the denominator (i.e. _denom or _d) + +Examples: +- To select cells in cluster 5 for the numerator set `'type_n': 'meta'`, `'subtype_n': 'cluster'`, `'group_num': 'Cluster 5'` +- To select cells in a saved manual selection for the numerator set `'type_n': 'saved_selection'`, `'group_num': 'name_of_selection'` +- To select a specific set of cell ids for the numerator set `'type_n': 'current'`, `'group_num': list of cell ids` + +Posted data structure: +``` +{ + 'type_n': either 'current', 'meta', or 'saved_selection' + 'type_d': either 'remainder', 'meta', or 'saved_selection' + 'subtype_n': which meta-data variable to group cells by if type_n is 'meta' + 'subtype_d': which meta-data variable to group cells by if type_d is 'meta' + 'group_num': list of cell ids (if type_n is 'current') OR name of saved selection (if type_n is 'saved_selection') + OR value of categorical meta-data variable (if type_n is 'meta') + 'group_denom': same behavior as 'group_num' + 'min_cells': (int) pre-filter genes expressed in less than this many cells + 'subsample_groups': (bool), whether or not to subsample each comparison group first + 'subsample_N': (int) size of the groups after subsampling. Ignored if 'subsample_groups' is false +} +``` + +Response structure: + +DE Results table with {'column name' -> list of values} + +``` +{ + 'Feature': list of feature (gene or protein) names + 'Type': list of either 'Gene' or 'Protein' + 'logFC': list of log-fold-change values + 'stat': list of AUC values + 'pval': list of FDR-corrected p-values +} +``` + + +# GET: /Clusters/MetaLevels +The display of the top-left area for signatures/proteins/meta-data depends on the selected +grouping variable in the dropdown. Commands scoped to a particular grouping variable are +nested under "/Clusters". + +This call returns a list of grouping variables and the levels/categories associated with them. + +Response structure: +``` + { + 'name of variable': [list of str - values this variable can take], + 'name of variable': [list of str - values this variable can take], + 'Cell Type': ['CD4+', 'CD8+', 'NK'], # For example + } +``` + +# GET: /Clusters//SigProjMatrix/Normal +Returns matrices consisting of test statistic and p-value for 1 vs. all differential signature +tests and for local autocorrelation. + +First column is "Score" and values are for local autocorrelation. Statistic is the 1 - Geary's C. + +Other columns are for 1 vs. all differential signature tests for each value in the selected grouping +variable in the dropdown. Test statistic are the AUC values from a ranksums test. P-values also +from this test. + +Response structure: +``` + { + 'sig_labels': [list of str] # Rows of matrices in zscores and pvals + 'proj_labels': [list of str] # Columns of the matrices in zscores and pvals + 'zscores': [list of list of number] # signatures x cell group (+ 'Score') matrix of test statistics + 'pvals': [list of list of number] # signatures x cell group (+ 'Score') matrix of p-values + } +``` + +# GET: /Clusters//SigProjMatrix/Meta +Same as `/Clusters//SigProjMatrix/Normal`, but for meta-data variables + +Response structure: +``` + { + 'sig_labels': [list of str] # Rows of matrices in zscores and pvals + 'proj_labels': [list of str] # Columns of the matrices in zscores and pvals + 'zscores': [list of list of number] # variables x cell group (+ 'Score') matrix of test statistics + 'pvals': [list of list of number] # variables x cell group (+ 'Score') matrix of p-values + } +``` +# GET: /Clusters//ProteinMatrix +Same as `/Clusters//SigProjMatrix/Normal`, but for CITE proteins + +Response structure: +``` + { + 'sig_labels': [list of str] # Rows of matrices in zscores and pvals + 'proj_labels': [list of str] # Columns of the matrices in zscores and pvals + 'zscores': [list of list of number] # proteins x cell group (+ 'Score') matrix of test statistics + 'pvals': [list of list of number] # proteins x cell group (+ 'Score') matrix of p-values + } +``` + +# GET: /Clusters/list +Not used anymore + +# GET: /Clusters//Cells +Not used anymore + + +# GET: /Expression/Genes/List +Retrieves a list of genes for which expression values can be plotted. +Used to populate the dropdown in the 'Genes' tab. + +Response structure: +``` +[list of str - gene names] +``` +# GET: /Expression/Gene/ +Gets the per-cell expression of the gene specified by ``. +Expression values returned are on a log2 scale. + +Response structure: +Items in 'values' correspond to the cells in 'cells' in order +``` + { + 'cells': [list of str - cell identifiers], + 'values': [list of number - gene expression values], + } +``` + +# GET: /Cell//Meta +Retrieves meta-data information for an individual cell specified by `` + +Response structure: +``` + { + 'variable name': value (str or number), + 'variable name': value (str or number), + 'variable name': value (str or number), + ... + } +``` + +# POST: /Cells/Meta +Retrieves meta-data information for a group of cells + +Posted data structure +``` +[list of cell id] +``` + +Response structure: +``` + { + 'numeric': { + '': { + 'Min': , + 'Median': , + 'Max': , + }, + '': { + 'Min': , + 'Median': , + 'Max': , + }, + # Repeat for additional numeric meta-data variables + }, + 'factor': { + '': { + '': number (proportion of cells assigned to this level, + '': number (proportion of cells assigned to this level, + '': number (proportion of cells assigned to this level, + ... + } + # Repeat for additional factor meta-data variables + } + } +``` + +# GET: /Cells/Selections +Used when loading a selection of cells. + +Response structure: +``` +[list of str - names of saved selections] +``` + +# GET: /Cells/Selections/ +Retrieves the cells associated with the selection, `` + +Response structure: +``` +[list of str - cell ids in the indicated cell selection] +``` +# POST: /Cells/Selections/ +Saves a cell selection with name `` + +``` +[list of str - cell ids to be assigned to this cell selection] +``` + +# GET: /Tree/Projections/list +Get the list of different tree layouts that are available +Used to populate the 'Projection' dropdown under the 'Trajectories' view + +R version: returns the names of object@TrajectoryProjections + +Response structure: +``` +[list of str - names of tree projections] +``` + +# GET: /Tree/Projections//coordinates +Returns the coordinates for the tree layout `` in addition +to the position of individual cells + +Response structure: +``` + [ + [ + [, , ], # coordinates for individual cells + [, , ], + [, , ], + ... + ], + [ + [, ], # coordinates for internal tree nodes + [, ], + [, ], + ... + ], + [list of list of number] # 0/1 adjacency matrix for internal tree nodes + ] +``` + + +# GET: /Tree/SigProjMatrix/Normal +Returns matrices consisting of test statistic and p-value trajectory autocorrelation +Format is similar to `/Clusters//SigProjMatrix/Normal`, but without +the 1 vs all test results. + +'zscores' and 'pvals' matrices have just a single column + +Response structure: +``` + { + 'sig_labels': [list of str] # Rows of matrices in zscores and pvals + 'proj_labels': ["Score"], + 'zscores': [list of list of number] # signatures x 1 matrix of test statistics + 'pvals': [list of list of number] # signatures x 1 matrix of p-values + } +``` + +# GET: /Tree/SigProjMatrix/Meta +Same as `/Tree/SigProjMatrix/Normal` but for meta-data variables + +'zscores' and 'pvals' matrices have just a single column + +Response structure: +``` + { + 'sig_labels': [list of str] # Rows of matrices in zscores and pvals + 'proj_labels': ["Score"], + 'zscores': [list of list of number] # variables x 1 matrix of test statistics + 'pvals': [list of list of number] # variables x 1 matrix of p-values + } +``` + +# GET: /Tree/ProteinMatrix +Same as `/Tree/SigProjMatrix/Normal` but for CITE protein expression values + +'zscores' and 'pvals' matrices have just a single column + +Response structure: +``` + { + 'sig_labels': [list of str] # Rows of matrices in zscores and pvals + 'proj_labels': ["Score"], + 'zscores': [list of list of number] # proteins x 1 matrix of test statistics + 'pvals': [list of list of number] # proteins x 1 matrix of p-values + } +``` From 91183ff5f835a9f962d1faf9e011f0907d86b169 Mon Sep 17 00:00:00 2001 From: Yanay1 Date: Wed, 5 May 2021 15:04:52 -0700 Subject: [PATCH 29/62] updating vignettes --- vignettes/metastasisPhyloVision.Rmd | 2 +- vignettes/phlyoVision.Rmd | 1 + vignettes/spatialHotspot.Rmd | 2 +- 3 files changed, 3 insertions(+), 2 deletions(-) diff --git a/vignettes/metastasisPhyloVision.Rmd b/vignettes/metastasisPhyloVision.Rmd index fa1fee5d..5f3e5e97 100644 --- a/vignettes/metastasisPhyloVision.Rmd +++ b/vignettes/metastasisPhyloVision.Rmd @@ -5,7 +5,7 @@ output: html_document ```{r setup, include=FALSE} knitr::opts_chunk$set(echo = TRUE) -devtools::load_all("/home/eecs/yanayrosen/VISION/") # change to just load VISION +library(VISION) library(ape) library(reticulate) ``` diff --git a/vignettes/phlyoVision.Rmd b/vignettes/phlyoVision.Rmd index f2c6e28f..1aed73d8 100644 --- a/vignettes/phlyoVision.Rmd +++ b/vignettes/phlyoVision.Rmd @@ -8,6 +8,7 @@ output: html_document ```{r setup, include=FALSE} knitr::opts_chunk$set(echo = TRUE) devtools::load_all("~/Desktop/VISION/") # change to just load VISION +library(VISION) library(ape) library(reticulate) ``` diff --git a/vignettes/spatialHotspot.Rmd b/vignettes/spatialHotspot.Rmd index a0c819bd..6b84cae3 100644 --- a/vignettes/spatialHotspot.Rmd +++ b/vignettes/spatialHotspot.Rmd @@ -7,7 +7,7 @@ output: html_document ```{r setup, include=FALSE} knitr::opts_chunk$set(echo = TRUE) -devtools::load_all("~/Desktop/VISION/") # change to just load VISION +library(VISION) library(reticulate) ``` From 1f077ad3ccd830ec7718c655439afde955f898bf Mon Sep 17 00:00:00 2001 From: Yanay1 Date: Wed, 5 May 2021 15:05:33 -0700 Subject: [PATCH 30/62] updating vignettes --- vignettes/metastasisPhyloVision.Rmd | 77 ----------------------------- 1 file changed, 77 deletions(-) delete mode 100644 vignettes/metastasisPhyloVision.Rmd diff --git a/vignettes/metastasisPhyloVision.Rmd b/vignettes/metastasisPhyloVision.Rmd deleted file mode 100644 index 5f3e5e97..00000000 --- a/vignettes/metastasisPhyloVision.Rmd +++ /dev/null @@ -1,77 +0,0 @@ ---- -title: "metastasis" -output: html_document ---- - -```{r setup, include=FALSE} -knitr::opts_chunk$set(echo = TRUE) -library(VISION) -library(ape) -library(reticulate) -``` - -## R Markdown - -This is an R Markdown document. Markdown is a simple formatting syntax for authoring HTML, PDF, and MS Word documents. For more details on using R Markdown see . - -When you click the **Knit** button a document will be generated that includes both content as well as the output of any embedded R code chunks within the document. You can embed an R code chunk like this: - -## Creating a Phylo Vision Object with a Tree - -Vision objects now support dendrograms for visualization and analysis. To create the Phylo-VISION object, you need all of the same data, an expression matrix, and metadata and/or signatures, but you also include a tree object from the Ape package. -```{r create} -# Read the expression and meta data -expr <- read_10x(expression = "/data/yosef2/users/mattjones/projects/PhyloVision/data/metastasis_data/GRCh38/matrix.mtx", - genes = "/data/yosef2/users/mattjones/projects/PhyloVision/data/metastasis_data/GRCh38/genes.tsv", - barcodes = "/data/yosef2/users/mattjones/projects/PhyloVision/data/metastasis_data/GRCh38/barcodes.tsv") - - -barcodes <- read.table("/data/yosef2/users/mattjones/projects/PhyloVision/data/metastasis_data/GRCh38/barcodes.tsv", check.names = FALSE, sep="\t") -latent <- read.table("/data/yosef2/users/mattjones/projects/PhyloVision/data/metastasis_data/latent.csv", check.names=FALSE, sep="\t", row.names = 1, header=TRUE) -row.names(latent) <- barcodes[, 1] - -meta <- read.table("/data/yosef2/users/mattjones/projects/PhyloVision/data/metastasis_data/GSM4905335_meta.5k.tsv.gz", check.names = FALSE, sep = "\t", row.names = 1, header=TRUE) -# meta$Cell_Type <- as.factor(meta$Cell_Type) -# Signature file -sigs = c("c5.go.bp.v7.2.symbols.gmt", "h.all.v5.2.symbols.gmt", "c4.cgn.v7.2.symbols.gmt") - -# Read the trees -lg7_tree <- read.tree("/data/yosef2/users/mattjones/projects/PhyloVision/data/metastasis_data/lg7_tree_hybrid_priors.alleleThresh.processed.txt") -lg4_tree <- read.tree("/data/yosef2/users/mattjones/projects/PhyloVision/data/metastasis_data/lg4_tree_hybrid_priors.alleleThresh.processed.txt") - -# Subset trees with expression -lg7_barcodes <- intersect(lg7_tree$tip.label, colnames(expr)) -lg4_barcodes <- intersect(lg4_tree$tip.label, colnames(expr)) - -lg7_tree <- keep.tip(lg7_tree, lg7_barcodes) -lg4_tree <- keep.tip(lg4_tree, lg4_barcodes) - -# Collapse one mutations -lg7_tree <- collapse.singles(lg7_tree) -lg4_tree <- collapse.singles(lg4_tree) - -expr_lg7 <- expr[, lg7_barcodes] -expr_lg4 <- expr[, lg4_barcodes] - -latent_lg7 <- latent[lg7_barcodes,] -latent_lg4 <- latent[lg4_barcodes,] - -meta_lg7 <- meta[lg7_barcodes,] -meta_lg4 <- meta[lg4_barcodes,] - -# Construct the Vision object -vis_lg7 <- PhyloVision(tree=lg7_tree, data=expr_lg7, latentSpace=latent_lg7, signatures=sigs, meta=meta_lg7, num_neighbors=40, projection_genes="threshold", sig_gene_threshold=0.05, projection_methods=c("tSNE30", "tSNE10", "UMAP")) -vis_lg4 <- PhyloVision(tree=lg4_tree, data=expr_lg4, latentSpace=latent_lg4, signatures=sigs, meta=meta_lg4, num_neighbors=40, projection_genes="threshold", sig_gene_threshold=0.05, projection_methods=c("tSNE30", "tSNE10", "UMAP")) -``` -Next, we can perform the normal Vision analysis using the tree as the latent space. - -```{r analyze} -vis_lg7 <- phyloAnalyze(vis_lg7) -vis_lg4 <- phyloAnalyze(vis_lg4) -``` - -We can also perform Hotspot module analysis. -```{r hotspot} -vis_lg7 <- 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n.__actions__=Mr(this.__actions__),n.__dir__=this.__dir__,n.__filtered__=this.__filtered__,n.__iteratees__=Mr(this.__iteratees__),n.__takeCount__=this.__takeCount__,n.__views__=Mr(this.__views__), -n},Mn.prototype.reverse=function(){if(this.__filtered__){var n=new Mn(this);n.__dir__=-1,n.__filtered__=true}else n=this.clone(),n.__dir__*=-1;return n},Mn.prototype.value=function(){var n,t=this.__wrapped__.value(),r=this.__dir__,e=af(t),u=0>r,i=e?t.length:0;n=i;for(var o=this.__views__,f=0,c=-1,a=o.length;++c=this.__values__.length;return{done:n,value:n?F:this.__values__[this.__index__++]}},On.prototype.plant=function(n){for(var t,r=this;r instanceof Sn;){var e=Pe(r);e.__index__=0,e.__values__=F,t?u.__wrapped__=e:t=e;var u=e,r=r.__wrapped__}return u.__wrapped__=n,t},On.prototype.reverse=function(){var n=this.__wrapped__;return n instanceof Mn?(this.__actions__.length&&(n=new Mn(this)),n=n.reverse(),n.__actions__.push({func:nu,args:[Je],thisArg:F}),new zn(n,this.__chain__)):this.thru(Je); -},On.prototype.toJSON=On.prototype.valueOf=On.prototype.value=function(){return kr(this.__wrapped__,this.__actions__)},On.prototype.first=On.prototype.head,Ai&&(On.prototype[Ai]=tu),On}();typeof define=="function"&&typeof define.amd=="object"&&define.amd?(Zn._=it, define(function(){return it})):Vn?((Vn.exports=it)._=it,qn._=it):Zn._=it}).call(this); \ No newline at end of file + ;(function() { + + /** Used as a safe reference for `undefined` in pre-ES5 environments. */ + var undefined; + + /** Used as the semantic version number. */ + var VERSION = '4.17.21'; + + /** Used as the size to enable large array optimizations. */ + var LARGE_ARRAY_SIZE = 200; + + /** Error message constants. */ + var CORE_ERROR_TEXT = 'Unsupported core-js use. Try https://npms.io/search?q=ponyfill.', + FUNC_ERROR_TEXT = 'Expected a function', + INVALID_TEMPL_VAR_ERROR_TEXT = 'Invalid `variable` option passed into `_.template`'; + + /** Used to stand-in for `undefined` hash values. */ + var HASH_UNDEFINED = '__lodash_hash_undefined__'; + + /** Used as the maximum memoize cache size. */ + var MAX_MEMOIZE_SIZE = 500; + + /** Used as the internal argument placeholder. */ + var PLACEHOLDER = '__lodash_placeholder__'; + + /** Used to compose bitmasks for cloning. */ + var CLONE_DEEP_FLAG = 1, + CLONE_FLAT_FLAG = 2, + CLONE_SYMBOLS_FLAG = 4; + + /** Used to compose bitmasks for value comparisons. */ + var COMPARE_PARTIAL_FLAG = 1, + COMPARE_UNORDERED_FLAG = 2; + + /** Used to compose bitmasks for function metadata. */ + var WRAP_BIND_FLAG = 1, + WRAP_BIND_KEY_FLAG = 2, + WRAP_CURRY_BOUND_FLAG = 4, + WRAP_CURRY_FLAG = 8, + WRAP_CURRY_RIGHT_FLAG = 16, + WRAP_PARTIAL_FLAG = 32, + WRAP_PARTIAL_RIGHT_FLAG = 64, + WRAP_ARY_FLAG = 128, + WRAP_REARG_FLAG = 256, + WRAP_FLIP_FLAG = 512; + + /** Used as default options for `_.truncate`. */ + var DEFAULT_TRUNC_LENGTH = 30, + DEFAULT_TRUNC_OMISSION = '...'; + + /** Used to detect hot functions by number of calls within a span of milliseconds. */ + var HOT_COUNT = 800, + HOT_SPAN = 16; + + /** Used to indicate the type of lazy iteratees. */ + var LAZY_FILTER_FLAG = 1, + LAZY_MAP_FLAG = 2, + LAZY_WHILE_FLAG = 3; + + /** Used as references for various `Number` constants. */ + var INFINITY = 1 / 0, + MAX_SAFE_INTEGER = 9007199254740991, + MAX_INTEGER = 1.7976931348623157e+308, + NAN = 0 / 0; + + /** Used as references for the maximum length and index of an array. */ + var MAX_ARRAY_LENGTH = 4294967295, + MAX_ARRAY_INDEX = MAX_ARRAY_LENGTH - 1, + HALF_MAX_ARRAY_LENGTH = MAX_ARRAY_LENGTH >>> 1; + + /** Used to associate wrap methods with their bit flags. */ + var wrapFlags = [ + ['ary', WRAP_ARY_FLAG], + ['bind', WRAP_BIND_FLAG], + ['bindKey', WRAP_BIND_KEY_FLAG], + ['curry', WRAP_CURRY_FLAG], + ['curryRight', WRAP_CURRY_RIGHT_FLAG], + ['flip', WRAP_FLIP_FLAG], + ['partial', WRAP_PARTIAL_FLAG], + ['partialRight', WRAP_PARTIAL_RIGHT_FLAG], + ['rearg', WRAP_REARG_FLAG] + ]; + + /** `Object#toString` result references. */ + var argsTag = '[object Arguments]', + arrayTag = '[object Array]', + asyncTag = '[object AsyncFunction]', + boolTag = '[object Boolean]', + dateTag = '[object Date]', + domExcTag = '[object DOMException]', + errorTag = '[object Error]', + funcTag = '[object Function]', + genTag = '[object GeneratorFunction]', + mapTag = '[object Map]', + numberTag = '[object Number]', + nullTag = '[object Null]', + objectTag = '[object Object]', + promiseTag = '[object Promise]', + proxyTag = '[object Proxy]', + regexpTag = '[object RegExp]', + setTag = '[object Set]', + stringTag = '[object String]', + symbolTag = '[object Symbol]', + undefinedTag = '[object Undefined]', + weakMapTag = '[object WeakMap]', + weakSetTag = '[object WeakSet]'; + + var arrayBufferTag = '[object ArrayBuffer]', + dataViewTag = '[object DataView]', + float32Tag = '[object Float32Array]', + float64Tag = '[object Float64Array]', + int8Tag = '[object Int8Array]', + int16Tag = '[object Int16Array]', + int32Tag = '[object Int32Array]', + uint8Tag = '[object Uint8Array]', + uint8ClampedTag = '[object Uint8ClampedArray]', + uint16Tag = '[object Uint16Array]', + uint32Tag = '[object Uint32Array]'; + + /** Used to match empty string literals in compiled template source. */ + var reEmptyStringLeading = /\b__p \+= '';/g, + reEmptyStringMiddle = /\b(__p \+=) '' \+/g, + reEmptyStringTrailing = /(__e\(.*?\)|\b__t\)) \+\n'';/g; + + /** Used to match HTML entities and HTML characters. */ + var reEscapedHtml = /&(?:amp|lt|gt|quot|#39);/g, + reUnescapedHtml = /[&<>"']/g, + reHasEscapedHtml = RegExp(reEscapedHtml.source), + reHasUnescapedHtml = RegExp(reUnescapedHtml.source); + + /** Used to match template delimiters. */ + var reEscape = /<%-([\s\S]+?)%>/g, + reEvaluate = /<%([\s\S]+?)%>/g, + reInterpolate = /<%=([\s\S]+?)%>/g; + + /** Used to match property names within property paths. */ + var reIsDeepProp = /\.|\[(?:[^[\]]*|(["'])(?:(?!\1)[^\\]|\\.)*?\1)\]/, + reIsPlainProp = /^\w*$/, + rePropName = /[^.[\]]+|\[(?:(-?\d+(?:\.\d+)?)|(["'])((?:(?!\2)[^\\]|\\.)*?)\2)\]|(?=(?:\.|\[\])(?:\.|\[\]|$))/g; + + /** + * Used to match `RegExp` + * [syntax characters](http://ecma-international.org/ecma-262/7.0/#sec-patterns). + */ + var reRegExpChar = /[\\^$.*+?()[\]{}|]/g, + reHasRegExpChar = RegExp(reRegExpChar.source); + + /** Used to match leading whitespace. */ + var reTrimStart = /^\s+/; + + /** Used to match a single whitespace character. */ + var reWhitespace = /\s/; + + /** Used to match wrap detail comments. */ + var reWrapComment = /\{(?:\n\/\* \[wrapped with .+\] \*\/)?\n?/, + reWrapDetails = /\{\n\/\* \[wrapped with (.+)\] \*/, + reSplitDetails = /,? & /; + + /** Used to match words composed of alphanumeric characters. */ + var reAsciiWord = /[^\x00-\x2f\x3a-\x40\x5b-\x60\x7b-\x7f]+/g; + + /** + * Used to validate the `validate` option in `_.template` variable. + * + * Forbids characters which could potentially change the meaning of the function argument definition: + * - "()," (modification of function parameters) + * - "=" (default value) + * - "[]{}" (destructuring of function parameters) + * - "/" (beginning of a comment) + * - whitespace + */ + var reForbiddenIdentifierChars = /[()=,{}\[\]\/\s]/; + + /** Used to match backslashes in property paths. */ + var reEscapeChar = /\\(\\)?/g; + + /** + * Used to match + * [ES template delimiters](http://ecma-international.org/ecma-262/7.0/#sec-template-literal-lexical-components). + */ + var reEsTemplate = /\$\{([^\\}]*(?:\\.[^\\}]*)*)\}/g; + + /** Used to match `RegExp` flags from their coerced string values. */ + var reFlags = /\w*$/; + + /** Used to detect bad signed hexadecimal string values. */ + var reIsBadHex = /^[-+]0x[0-9a-f]+$/i; + + /** Used to detect binary string values. */ + var reIsBinary = /^0b[01]+$/i; + + /** Used to detect host constructors (Safari). */ + var reIsHostCtor = /^\[object .+?Constructor\]$/; + + /** Used to detect octal string values. */ + var reIsOctal = /^0o[0-7]+$/i; + + /** Used to detect unsigned integer values. */ + var reIsUint = /^(?:0|[1-9]\d*)$/; + + /** Used to match Latin Unicode letters (excluding mathematical operators). */ + var reLatin = /[\xc0-\xd6\xd8-\xf6\xf8-\xff\u0100-\u017f]/g; + + /** Used to ensure capturing order of template delimiters. */ + var reNoMatch = /($^)/; + + /** Used to match unescaped characters in compiled string literals. */ + var reUnescapedString = /['\n\r\u2028\u2029\\]/g; + + /** Used to compose unicode character classes. */ + var rsAstralRange = '\\ud800-\\udfff', + rsComboMarksRange = '\\u0300-\\u036f', + reComboHalfMarksRange = '\\ufe20-\\ufe2f', + rsComboSymbolsRange = '\\u20d0-\\u20ff', + rsComboRange = rsComboMarksRange + reComboHalfMarksRange + rsComboSymbolsRange, + rsDingbatRange = '\\u2700-\\u27bf', + rsLowerRange = 'a-z\\xdf-\\xf6\\xf8-\\xff', + rsMathOpRange = '\\xac\\xb1\\xd7\\xf7', + rsNonCharRange = '\\x00-\\x2f\\x3a-\\x40\\x5b-\\x60\\x7b-\\xbf', + rsPunctuationRange = '\\u2000-\\u206f', + rsSpaceRange = ' \\t\\x0b\\f\\xa0\\ufeff\\n\\r\\u2028\\u2029\\u1680\\u180e\\u2000\\u2001\\u2002\\u2003\\u2004\\u2005\\u2006\\u2007\\u2008\\u2009\\u200a\\u202f\\u205f\\u3000', + rsUpperRange = 'A-Z\\xc0-\\xd6\\xd8-\\xde', + rsVarRange = '\\ufe0e\\ufe0f', + rsBreakRange = rsMathOpRange + rsNonCharRange + rsPunctuationRange + rsSpaceRange; + + /** Used to compose unicode capture groups. */ + var rsApos = "['\u2019]", + rsAstral = '[' + rsAstralRange + ']', + rsBreak = '[' + rsBreakRange + ']', + rsCombo = '[' + rsComboRange + ']', + rsDigits = '\\d+', + rsDingbat = '[' + rsDingbatRange + ']', + rsLower = '[' + rsLowerRange + ']', + rsMisc = '[^' + rsAstralRange + rsBreakRange + rsDigits + rsDingbatRange + rsLowerRange + rsUpperRange + ']', + rsFitz = '\\ud83c[\\udffb-\\udfff]', + rsModifier = '(?:' + rsCombo + '|' + rsFitz + ')', + rsNonAstral = '[^' + rsAstralRange + ']', + rsRegional = '(?:\\ud83c[\\udde6-\\uddff]){2}', + rsSurrPair = '[\\ud800-\\udbff][\\udc00-\\udfff]', + rsUpper = '[' + rsUpperRange + ']', + rsZWJ = '\\u200d'; + + /** Used to compose unicode regexes. */ + var rsMiscLower = '(?:' + rsLower + '|' + rsMisc + ')', + rsMiscUpper = '(?:' + rsUpper + '|' + rsMisc + ')', + rsOptContrLower = '(?:' + rsApos + '(?:d|ll|m|re|s|t|ve))?', + rsOptContrUpper = '(?:' + rsApos + '(?:D|LL|M|RE|S|T|VE))?', + reOptMod = rsModifier + '?', + rsOptVar = '[' + rsVarRange + ']?', + rsOptJoin = '(?:' + rsZWJ + '(?:' + [rsNonAstral, rsRegional, rsSurrPair].join('|') + ')' + rsOptVar + reOptMod + ')*', + rsOrdLower = '\\d*(?:1st|2nd|3rd|(?![123])\\dth)(?=\\b|[A-Z_])', + rsOrdUpper = '\\d*(?:1ST|2ND|3RD|(?![123])\\dTH)(?=\\b|[a-z_])', + rsSeq = rsOptVar + reOptMod + rsOptJoin, + rsEmoji = '(?:' + [rsDingbat, rsRegional, rsSurrPair].join('|') + ')' + rsSeq, + rsSymbol = '(?:' + [rsNonAstral + rsCombo + '?', rsCombo, rsRegional, rsSurrPair, rsAstral].join('|') + ')'; + + /** Used to match apostrophes. */ + var reApos = RegExp(rsApos, 'g'); + + /** + * Used to match [combining diacritical marks](https://en.wikipedia.org/wiki/Combining_Diacritical_Marks) and + * [combining diacritical marks for symbols](https://en.wikipedia.org/wiki/Combining_Diacritical_Marks_for_Symbols). + */ + var reComboMark = RegExp(rsCombo, 'g'); + + /** Used to match [string symbols](https://mathiasbynens.be/notes/javascript-unicode). */ + var reUnicode = RegExp(rsFitz + '(?=' + rsFitz + ')|' + rsSymbol + rsSeq, 'g'); + + /** Used to match complex or compound words. */ + var reUnicodeWord = RegExp([ + rsUpper + '?' + rsLower + '+' + rsOptContrLower + '(?=' + [rsBreak, rsUpper, '$'].join('|') + ')', + rsMiscUpper + '+' + rsOptContrUpper + '(?=' + [rsBreak, rsUpper + rsMiscLower, '$'].join('|') + ')', + rsUpper + '?' + rsMiscLower + '+' + rsOptContrLower, + rsUpper + '+' + rsOptContrUpper, + rsOrdUpper, + rsOrdLower, + rsDigits, + rsEmoji + ].join('|'), 'g'); + + /** Used to detect strings with [zero-width joiners or code points from the astral planes](http://eev.ee/blog/2015/09/12/dark-corners-of-unicode/). */ + var reHasUnicode = RegExp('[' + rsZWJ + rsAstralRange + rsComboRange + rsVarRange + ']'); + + /** Used to detect strings that need a more robust regexp to match words. */ + var reHasUnicodeWord = /[a-z][A-Z]|[A-Z]{2}[a-z]|[0-9][a-zA-Z]|[a-zA-Z][0-9]|[^a-zA-Z0-9 ]/; + + /** Used to assign default `context` object properties. */ + var contextProps = [ + 'Array', 'Buffer', 'DataView', 'Date', 'Error', 'Float32Array', 'Float64Array', + 'Function', 'Int8Array', 'Int16Array', 'Int32Array', 'Map', 'Math', 'Object', + 'Promise', 'RegExp', 'Set', 'String', 'Symbol', 'TypeError', 'Uint8Array', + 'Uint8ClampedArray', 'Uint16Array', 'Uint32Array', 'WeakMap', + '_', 'clearTimeout', 'isFinite', 'parseInt', 'setTimeout' + ]; + + /** Used to make template sourceURLs easier to identify. */ + var templateCounter = -1; + + /** Used to identify `toStringTag` values of typed arrays. */ + var typedArrayTags = {}; + typedArrayTags[float32Tag] = typedArrayTags[float64Tag] = + typedArrayTags[int8Tag] = typedArrayTags[int16Tag] = + typedArrayTags[int32Tag] = typedArrayTags[uint8Tag] = + typedArrayTags[uint8ClampedTag] = typedArrayTags[uint16Tag] = + typedArrayTags[uint32Tag] = true; + typedArrayTags[argsTag] = typedArrayTags[arrayTag] = + typedArrayTags[arrayBufferTag] = typedArrayTags[boolTag] = + typedArrayTags[dataViewTag] = typedArrayTags[dateTag] = + typedArrayTags[errorTag] = typedArrayTags[funcTag] = + typedArrayTags[mapTag] = typedArrayTags[numberTag] = + typedArrayTags[objectTag] = typedArrayTags[regexpTag] = + typedArrayTags[setTag] = typedArrayTags[stringTag] = + typedArrayTags[weakMapTag] = false; + + /** Used to identify `toStringTag` values supported by `_.clone`. */ + var cloneableTags = {}; + cloneableTags[argsTag] = cloneableTags[arrayTag] = + cloneableTags[arrayBufferTag] = cloneableTags[dataViewTag] = + cloneableTags[boolTag] = cloneableTags[dateTag] = + cloneableTags[float32Tag] = cloneableTags[float64Tag] = + cloneableTags[int8Tag] = cloneableTags[int16Tag] = + cloneableTags[int32Tag] = cloneableTags[mapTag] = + cloneableTags[numberTag] = cloneableTags[objectTag] = + cloneableTags[regexpTag] = cloneableTags[setTag] = + cloneableTags[stringTag] = cloneableTags[symbolTag] = + cloneableTags[uint8Tag] = cloneableTags[uint8ClampedTag] = + cloneableTags[uint16Tag] = cloneableTags[uint32Tag] = true; + cloneableTags[errorTag] = cloneableTags[funcTag] = + cloneableTags[weakMapTag] = false; + + /** Used to map Latin Unicode letters to basic Latin letters. */ + var deburredLetters = { + // Latin-1 Supplement block. + '\xc0': 'A', '\xc1': 'A', '\xc2': 'A', '\xc3': 'A', '\xc4': 'A', '\xc5': 'A', + '\xe0': 'a', '\xe1': 'a', '\xe2': 'a', '\xe3': 'a', '\xe4': 'a', '\xe5': 'a', + '\xc7': 'C', '\xe7': 'c', + '\xd0': 'D', '\xf0': 'd', + '\xc8': 'E', '\xc9': 'E', '\xca': 'E', '\xcb': 'E', + '\xe8': 'e', '\xe9': 'e', '\xea': 'e', '\xeb': 'e', + '\xcc': 'I', '\xcd': 'I', '\xce': 'I', '\xcf': 'I', + '\xec': 'i', '\xed': 'i', '\xee': 'i', '\xef': 'i', + '\xd1': 'N', '\xf1': 'n', + '\xd2': 'O', '\xd3': 'O', '\xd4': 'O', '\xd5': 'O', '\xd6': 'O', '\xd8': 'O', + '\xf2': 'o', '\xf3': 'o', '\xf4': 'o', '\xf5': 'o', '\xf6': 'o', '\xf8': 'o', + '\xd9': 'U', '\xda': 'U', '\xdb': 'U', '\xdc': 'U', + '\xf9': 'u', '\xfa': 'u', '\xfb': 'u', '\xfc': 'u', + '\xdd': 'Y', '\xfd': 'y', '\xff': 'y', + '\xc6': 'Ae', '\xe6': 'ae', + '\xde': 'Th', '\xfe': 'th', + '\xdf': 'ss', + // Latin Extended-A block. + '\u0100': 'A', '\u0102': 'A', '\u0104': 'A', + '\u0101': 'a', '\u0103': 'a', '\u0105': 'a', + '\u0106': 'C', '\u0108': 'C', '\u010a': 'C', '\u010c': 'C', + '\u0107': 'c', '\u0109': 'c', '\u010b': 'c', '\u010d': 'c', + '\u010e': 'D', '\u0110': 'D', '\u010f': 'd', '\u0111': 'd', + '\u0112': 'E', '\u0114': 'E', '\u0116': 'E', '\u0118': 'E', '\u011a': 'E', + '\u0113': 'e', '\u0115': 'e', '\u0117': 'e', '\u0119': 'e', '\u011b': 'e', + '\u011c': 'G', '\u011e': 'G', '\u0120': 'G', '\u0122': 'G', + '\u011d': 'g', '\u011f': 'g', '\u0121': 'g', '\u0123': 'g', + '\u0124': 'H', '\u0126': 'H', '\u0125': 'h', '\u0127': 'h', + '\u0128': 'I', '\u012a': 'I', '\u012c': 'I', '\u012e': 'I', '\u0130': 'I', + '\u0129': 'i', '\u012b': 'i', '\u012d': 'i', '\u012f': 'i', '\u0131': 'i', + '\u0134': 'J', '\u0135': 'j', + '\u0136': 'K', '\u0137': 'k', '\u0138': 'k', + '\u0139': 'L', '\u013b': 'L', '\u013d': 'L', '\u013f': 'L', '\u0141': 'L', + '\u013a': 'l', '\u013c': 'l', '\u013e': 'l', '\u0140': 'l', '\u0142': 'l', + '\u0143': 'N', '\u0145': 'N', '\u0147': 'N', '\u014a': 'N', + '\u0144': 'n', '\u0146': 'n', '\u0148': 'n', '\u014b': 'n', + '\u014c': 'O', '\u014e': 'O', '\u0150': 'O', + '\u014d': 'o', '\u014f': 'o', '\u0151': 'o', + '\u0154': 'R', '\u0156': 'R', '\u0158': 'R', + '\u0155': 'r', '\u0157': 'r', '\u0159': 'r', + '\u015a': 'S', '\u015c': 'S', '\u015e': 'S', '\u0160': 'S', + '\u015b': 's', '\u015d': 's', '\u015f': 's', '\u0161': 's', + '\u0162': 'T', '\u0164': 'T', '\u0166': 'T', + '\u0163': 't', '\u0165': 't', '\u0167': 't', + '\u0168': 'U', '\u016a': 'U', '\u016c': 'U', '\u016e': 'U', '\u0170': 'U', '\u0172': 'U', + '\u0169': 'u', '\u016b': 'u', '\u016d': 'u', '\u016f': 'u', '\u0171': 'u', '\u0173': 'u', + '\u0174': 'W', '\u0175': 'w', + '\u0176': 'Y', '\u0177': 'y', '\u0178': 'Y', + '\u0179': 'Z', '\u017b': 'Z', '\u017d': 'Z', + '\u017a': 'z', '\u017c': 'z', '\u017e': 'z', + '\u0132': 'IJ', '\u0133': 'ij', + '\u0152': 'Oe', '\u0153': 'oe', + '\u0149': "'n", '\u017f': 's' + }; + + /** Used to map characters to HTML entities. */ + var htmlEscapes = { + '&': '&', + '<': '<', + '>': '>', + '"': '"', + "'": ''' + }; + + /** Used to map HTML entities to characters. */ + var htmlUnescapes = { + '&': '&', + '<': '<', + '>': '>', + '"': '"', + ''': "'" + }; + + /** Used to escape characters for inclusion in compiled string literals. */ + var stringEscapes = { + '\\': '\\', + "'": "'", + '\n': 'n', + '\r': 'r', + '\u2028': 'u2028', + '\u2029': 'u2029' + }; + + /** Built-in method references without a dependency on `root`. */ + var freeParseFloat = parseFloat, + freeParseInt = parseInt; + + /** Detect free variable `global` from Node.js. */ + var freeGlobal = typeof global == 'object' && global && global.Object === Object && global; + + /** Detect free variable `self`. */ + var freeSelf = typeof self == 'object' && self && self.Object === Object && self; + + /** Used as a reference to the global object. */ + var root = freeGlobal || freeSelf || Function('return this')(); + + /** Detect free variable `exports`. */ + var freeExports = typeof exports == 'object' && exports && !exports.nodeType && exports; + + /** Detect free variable `module`. */ + var freeModule = freeExports && typeof module == 'object' && module && !module.nodeType && module; + + /** Detect the popular CommonJS extension `module.exports`. */ + var moduleExports = freeModule && freeModule.exports === freeExports; + + /** Detect free variable `process` from Node.js. */ + var freeProcess = moduleExports && freeGlobal.process; + + /** Used to access faster Node.js helpers. */ + var nodeUtil = (function() { + try { + // Use `util.types` for Node.js 10+. + var types = freeModule && freeModule.require && freeModule.require('util').types; + + if (types) { + return types; + } + + // Legacy `process.binding('util')` for Node.js < 10. + return freeProcess && freeProcess.binding && freeProcess.binding('util'); + } catch (e) {} + }()); + + /* Node.js helper references. */ + var nodeIsArrayBuffer = nodeUtil && nodeUtil.isArrayBuffer, + nodeIsDate = nodeUtil && nodeUtil.isDate, + nodeIsMap = nodeUtil && nodeUtil.isMap, + nodeIsRegExp = nodeUtil && nodeUtil.isRegExp, + nodeIsSet = nodeUtil && nodeUtil.isSet, + nodeIsTypedArray = nodeUtil && nodeUtil.isTypedArray; + + /*--------------------------------------------------------------------------*/ + + /** + * A faster alternative to `Function#apply`, this function invokes `func` + * with the `this` binding of `thisArg` and the arguments of `args`. + * + * @private + * @param {Function} func The function to invoke. + * @param {*} thisArg The `this` binding of `func`. + * @param {Array} args The arguments to invoke `func` with. + * @returns {*} Returns the result of `func`. + */ + function apply(func, thisArg, args) { + switch (args.length) { + case 0: return func.call(thisArg); + case 1: return func.call(thisArg, args[0]); + case 2: return func.call(thisArg, args[0], args[1]); + case 3: return func.call(thisArg, args[0], args[1], args[2]); + } + return func.apply(thisArg, args); + } + + /** + * A specialized version of `baseAggregator` for arrays. + * + * @private + * @param {Array} [array] The array to iterate over. + * @param {Function} setter The function to set `accumulator` values. + * @param {Function} iteratee The iteratee to transform keys. + * @param {Object} accumulator The initial aggregated object. + * @returns {Function} Returns `accumulator`. + */ + function arrayAggregator(array, setter, iteratee, accumulator) { + var index = -1, + length = array == null ? 0 : array.length; + + while (++index < length) { + var value = array[index]; + setter(accumulator, value, iteratee(value), array); + } + return accumulator; + } + + /** + * A specialized version of `_.forEach` for arrays without support for + * iteratee shorthands. + * + * @private + * @param {Array} [array] The array to iterate over. + * @param {Function} iteratee The function invoked per iteration. + * @returns {Array} Returns `array`. + */ + function arrayEach(array, iteratee) { + var index = -1, + length = array == null ? 0 : array.length; + + while (++index < length) { + if (iteratee(array[index], index, array) === false) { + break; + } + } + return array; + } + + /** + * A specialized version of `_.forEachRight` for arrays without support for + * iteratee shorthands. + * + * @private + * @param {Array} [array] The array to iterate over. + * @param {Function} iteratee The function invoked per iteration. + * @returns {Array} Returns `array`. + */ + function arrayEachRight(array, iteratee) { + var length = array == null ? 0 : array.length; + + while (length--) { + if (iteratee(array[length], length, array) === false) { + break; + } + } + return array; + } + + /** + * A specialized version of `_.every` for arrays without support for + * iteratee shorthands. + * + * @private + * @param {Array} [array] The array to iterate over. + * @param {Function} predicate The function invoked per iteration. + * @returns {boolean} Returns `true` if all elements pass the predicate check, + * else `false`. + */ + function arrayEvery(array, predicate) { + var index = -1, + length = array == null ? 0 : array.length; + + while (++index < length) { + if (!predicate(array[index], index, array)) { + return false; + } + } + return true; + } + + /** + * A specialized version of `_.filter` for arrays without support for + * iteratee shorthands. + * + * @private + * @param {Array} [array] The array to iterate over. + * @param {Function} predicate The function invoked per iteration. + * @returns {Array} Returns the new filtered array. + */ + function arrayFilter(array, predicate) { + var index = -1, + length = array == null ? 0 : array.length, + resIndex = 0, + result = []; + + while (++index < length) { + var value = array[index]; + if (predicate(value, index, array)) { + result[resIndex++] = value; + } + } + return result; + } + + /** + * A specialized version of `_.includes` for arrays without support for + * specifying an index to search from. + * + * @private + * @param {Array} [array] The array to inspect. + * @param {*} target The value to search for. + * @returns {boolean} Returns `true` if `target` is found, else `false`. + */ + function arrayIncludes(array, value) { + var length = array == null ? 0 : array.length; + return !!length && baseIndexOf(array, value, 0) > -1; + } + + /** + * This function is like `arrayIncludes` except that it accepts a comparator. + * + * @private + * @param {Array} [array] The array to inspect. + * @param {*} target The value to search for. + * @param {Function} comparator The comparator invoked per element. + * @returns {boolean} Returns `true` if `target` is found, else `false`. + */ + function arrayIncludesWith(array, value, comparator) { + var index = -1, + length = array == null ? 0 : array.length; + + while (++index < length) { + if (comparator(value, array[index])) { + return true; + } + } + return false; + } + + /** + * A specialized version of `_.map` for arrays without support for iteratee + * shorthands. + * + * @private + * @param {Array} [array] The array to iterate over. + * @param {Function} iteratee The function invoked per iteration. + * @returns {Array} Returns the new mapped array. + */ + function arrayMap(array, iteratee) { + var index = -1, + length = array == null ? 0 : array.length, + result = Array(length); + + while (++index < length) { + result[index] = iteratee(array[index], index, array); + } + return result; + } + + /** + * Appends the elements of `values` to `array`. + * + * @private + * @param {Array} array The array to modify. + * @param {Array} values The values to append. + * @returns {Array} Returns `array`. + */ + function arrayPush(array, values) { + var index = -1, + length = values.length, + offset = array.length; + + while (++index < length) { + array[offset + index] = values[index]; + } + return array; + } + + /** + * A specialized version of `_.reduce` for arrays without support for + * iteratee shorthands. + * + * @private + * @param {Array} [array] The array to iterate over. + * @param {Function} iteratee The function invoked per iteration. + * @param {*} [accumulator] The initial value. + * @param {boolean} [initAccum] Specify using the first element of `array` as + * the initial value. + * @returns {*} Returns the accumulated value. + */ + function arrayReduce(array, iteratee, accumulator, initAccum) { + var index = -1, + length = array == null ? 0 : array.length; + + if (initAccum && length) { + accumulator = array[++index]; + } + while (++index < length) { + accumulator = iteratee(accumulator, array[index], index, array); + } + return accumulator; + } + + /** + * A specialized version of `_.reduceRight` for arrays without support for + * iteratee shorthands. + * + * @private + * @param {Array} [array] The array to iterate over. + * @param {Function} iteratee The function invoked per iteration. + * @param {*} [accumulator] The initial value. + * @param {boolean} [initAccum] Specify using the last element of `array` as + * the initial value. + * @returns {*} Returns the accumulated value. + */ + function arrayReduceRight(array, iteratee, accumulator, initAccum) { + var length = array == null ? 0 : array.length; + if (initAccum && length) { + accumulator = array[--length]; + } + while (length--) { + accumulator = iteratee(accumulator, array[length], length, array); + } + return accumulator; + } + + /** + * A specialized version of `_.some` for arrays without support for iteratee + * shorthands. + * + * @private + * @param {Array} [array] The array to iterate over. + * @param {Function} predicate The function invoked per iteration. + * @returns {boolean} Returns `true` if any element passes the predicate check, + * else `false`. + */ + function arraySome(array, predicate) { + var index = -1, + length = array == null ? 0 : array.length; + + while (++index < length) { + if (predicate(array[index], index, array)) { + return true; + } + } + return false; + } + + /** + * Gets the size of an ASCII `string`. + * + * @private + * @param {string} string The string inspect. + * @returns {number} Returns the string size. + */ + var asciiSize = baseProperty('length'); + + /** + * Converts an ASCII `string` to an array. + * + * @private + * @param {string} string The string to convert. + * @returns {Array} Returns the converted array. + */ + function asciiToArray(string) { + return string.split(''); + } + + /** + * Splits an ASCII `string` into an array of its words. + * + * @private + * @param {string} The string to inspect. + * @returns {Array} Returns the words of `string`. + */ + function asciiWords(string) { + return string.match(reAsciiWord) || []; + } + + /** + * The base implementation of methods like `_.findKey` and `_.findLastKey`, + * without support for iteratee shorthands, which iterates over `collection` + * using `eachFunc`. + * + * @private + * @param {Array|Object} collection The collection to inspect. + * @param {Function} predicate The function invoked per iteration. + * @param {Function} eachFunc The function to iterate over `collection`. + * @returns {*} Returns the found element or its key, else `undefined`. + */ + function baseFindKey(collection, predicate, eachFunc) { + var result; + eachFunc(collection, function(value, key, collection) { + if (predicate(value, key, collection)) { + result = key; + return false; + } + }); + return result; + } + + /** + * The base implementation of `_.findIndex` and `_.findLastIndex` without + * support for iteratee shorthands. + * + * @private + * @param {Array} array The array to inspect. + * @param {Function} predicate The function invoked per iteration. + * @param {number} fromIndex The index to search from. + * @param {boolean} [fromRight] Specify iterating from right to left. + * @returns {number} Returns the index of the matched value, else `-1`. + */ + function baseFindIndex(array, predicate, fromIndex, fromRight) { + var length = array.length, + index = fromIndex + (fromRight ? 1 : -1); + + while ((fromRight ? index-- : ++index < length)) { + if (predicate(array[index], index, array)) { + return index; + } + } + return -1; + } + + /** + * The base implementation of `_.indexOf` without `fromIndex` bounds checks. + * + * @private + * @param {Array} array The array to inspect. + * @param {*} value The value to search for. + * @param {number} fromIndex The index to search from. + * @returns {number} Returns the index of the matched value, else `-1`. + */ + function baseIndexOf(array, value, fromIndex) { + return value === value + ? strictIndexOf(array, value, fromIndex) + : baseFindIndex(array, baseIsNaN, fromIndex); + } + + /** + * This function is like `baseIndexOf` except that it accepts a comparator. + * + * @private + * @param {Array} array The array to inspect. + * @param {*} value The value to search for. + * @param {number} fromIndex The index to search from. + * @param {Function} comparator The comparator invoked per element. + * @returns {number} Returns the index of the matched value, else `-1`. + */ + function baseIndexOfWith(array, value, fromIndex, comparator) { + var index = fromIndex - 1, + length = array.length; + + while (++index < length) { + if (comparator(array[index], value)) { + return index; + } + } + return -1; + } + + /** + * The base implementation of `_.isNaN` without support for number objects. + * + * @private + * @param {*} value The value to check. + * @returns {boolean} Returns `true` if `value` is `NaN`, else `false`. + */ + function baseIsNaN(value) { + return value !== value; + } + + /** + * The base implementation of `_.mean` and `_.meanBy` without support for + * iteratee shorthands. + * + * @private + * @param {Array} array The array to iterate over. + * @param {Function} iteratee The function invoked per iteration. + * @returns {number} Returns the mean. + */ + function baseMean(array, iteratee) { + var length = array == null ? 0 : array.length; + return length ? (baseSum(array, iteratee) / length) : NAN; + } + + /** + * The base implementation of `_.property` without support for deep paths. + * + * @private + * @param {string} key The key of the property to get. + * @returns {Function} Returns the new accessor function. + */ + function baseProperty(key) { + return function(object) { + return object == null ? undefined : object[key]; + }; + } + + /** + * The base implementation of `_.propertyOf` without support for deep paths. + * + * @private + * @param {Object} object The object to query. + * @returns {Function} Returns the new accessor function. + */ + function basePropertyOf(object) { + return function(key) { + return object == null ? undefined : object[key]; + }; + } + + /** + * The base implementation of `_.reduce` and `_.reduceRight`, without support + * for iteratee shorthands, which iterates over `collection` using `eachFunc`. + * + * @private + * @param {Array|Object} collection The collection to iterate over. + * @param {Function} iteratee The function invoked per iteration. + * @param {*} accumulator The initial value. + * @param {boolean} initAccum Specify using the first or last element of + * `collection` as the initial value. + * @param {Function} eachFunc The function to iterate over `collection`. + * @returns {*} Returns the accumulated value. + */ + function baseReduce(collection, iteratee, accumulator, initAccum, eachFunc) { + eachFunc(collection, function(value, index, collection) { + accumulator = initAccum + ? (initAccum = false, value) + : iteratee(accumulator, value, index, collection); + }); + return accumulator; + } + + /** + * The base implementation of `_.sortBy` which uses `comparer` to define the + * sort order of `array` and replaces criteria objects with their corresponding + * values. + * + * @private + * @param {Array} array The array to sort. + * @param {Function} comparer The function to define sort order. + * @returns {Array} Returns `array`. + */ + function baseSortBy(array, comparer) { + var length = array.length; + + array.sort(comparer); + while (length--) { + array[length] = array[length].value; + } + return array; + } + + /** + * The base implementation of `_.sum` and `_.sumBy` without support for + * iteratee shorthands. + * + * @private + * @param {Array} array The array to iterate over. + * @param {Function} iteratee The function invoked per iteration. + * @returns {number} Returns the sum. + */ + function baseSum(array, iteratee) { + var result, + index = -1, + length = array.length; + + while (++index < length) { + var current = iteratee(array[index]); + if (current !== undefined) { + result = result === undefined ? current : (result + current); + } + } + return result; + } + + /** + * The base implementation of `_.times` without support for iteratee shorthands + * or max array length checks. + * + * @private + * @param {number} n The number of times to invoke `iteratee`. + * @param {Function} iteratee The function invoked per iteration. + * @returns {Array} Returns the array of results. + */ + function baseTimes(n, iteratee) { + var index = -1, + result = Array(n); + + while (++index < n) { + result[index] = iteratee(index); + } + return result; + } + + /** + * The base implementation of `_.toPairs` and `_.toPairsIn` which creates an array + * of key-value pairs for `object` corresponding to the property names of `props`. + * + * @private + * @param {Object} object The object to query. + * @param {Array} props The property names to get values for. + * @returns {Object} Returns the key-value pairs. + */ + function baseToPairs(object, props) { + return arrayMap(props, function(key) { + return [key, object[key]]; + }); + } + + /** + * The base implementation of `_.trim`. + * + * @private + * @param {string} string The string to trim. + * @returns {string} Returns the trimmed string. + */ + function baseTrim(string) { + return string + ? string.slice(0, trimmedEndIndex(string) + 1).replace(reTrimStart, '') + : string; + } + + /** + * The base implementation of `_.unary` without support for storing metadata. + * + * @private + * @param {Function} func The function to cap arguments for. + * @returns {Function} Returns the new capped function. + */ + function baseUnary(func) { + return function(value) { + return func(value); + }; + } + + /** + * The base implementation of `_.values` and `_.valuesIn` which creates an + * array of `object` property values corresponding to the property names + * of `props`. + * + * @private + * @param {Object} object The object to query. + * @param {Array} props The property names to get values for. + * @returns {Object} Returns the array of property values. + */ + function baseValues(object, props) { + return arrayMap(props, function(key) { + return object[key]; + }); + } + + /** + * Checks if a `cache` value for `key` exists. + * + * @private + * @param {Object} cache The cache to query. + * @param {string} key The key of the entry to check. + * @returns {boolean} Returns `true` if an entry for `key` exists, else `false`. + */ + function cacheHas(cache, key) { + return cache.has(key); + } + + /** + * Used by `_.trim` and `_.trimStart` to get the index of the first string symbol + * that is not found in the character symbols. + * + * @private + * @param {Array} strSymbols The string symbols to inspect. + * @param {Array} chrSymbols The character symbols to find. + * @returns {number} Returns the index of the first unmatched string symbol. + */ + function charsStartIndex(strSymbols, chrSymbols) { + var index = -1, + length = strSymbols.length; + + while (++index < length && baseIndexOf(chrSymbols, strSymbols[index], 0) > -1) {} + return index; + } + + /** + * Used by `_.trim` and `_.trimEnd` to get the index of the last string symbol + * that is not found in the character symbols. + * + * @private + * @param {Array} strSymbols The string symbols to inspect. + * @param {Array} chrSymbols The character symbols to find. + * @returns {number} Returns the index of the last unmatched string symbol. + */ + function charsEndIndex(strSymbols, chrSymbols) { + var index = strSymbols.length; + + while (index-- && baseIndexOf(chrSymbols, strSymbols[index], 0) > -1) {} + return index; + } + + /** + * Gets the number of `placeholder` occurrences in `array`. + * + * @private + * @param {Array} array The array to inspect. + * @param {*} placeholder The placeholder to search for. + * @returns {number} Returns the placeholder count. + */ + function countHolders(array, placeholder) { + var length = array.length, + result = 0; + + while (length--) { + if (array[length] === placeholder) { + ++result; + } + } + return result; + } + + /** + * Used by `_.deburr` to convert Latin-1 Supplement and Latin Extended-A + * letters to basic Latin letters. + * + * @private + * @param {string} letter The matched letter to deburr. + * @returns {string} Returns the deburred letter. + */ + var deburrLetter = basePropertyOf(deburredLetters); + + /** + * Used by `_.escape` to convert characters to HTML entities. + * + * @private + * @param {string} chr The matched character to escape. + * @returns {string} Returns the escaped character. + */ + var escapeHtmlChar = basePropertyOf(htmlEscapes); + + /** + * Used by `_.template` to escape characters for inclusion in compiled string literals. + * + * @private + * @param {string} chr The matched character to escape. + * @returns {string} Returns the escaped character. + */ + function escapeStringChar(chr) { + return '\\' + stringEscapes[chr]; + } + + /** + * Gets the value at `key` of `object`. + * + * @private + * @param {Object} [object] The object to query. + * @param {string} key The key of the property to get. + * @returns {*} Returns the property value. + */ + function getValue(object, key) { + return object == null ? undefined : object[key]; + } + + /** + * Checks if `string` contains Unicode symbols. + * + * @private + * @param {string} string The string to inspect. + * @returns {boolean} Returns `true` if a symbol is found, else `false`. + */ + function hasUnicode(string) { + return reHasUnicode.test(string); + } + + /** + * Checks if `string` contains a word composed of Unicode symbols. + * + * @private + * @param {string} string The string to inspect. + * @returns {boolean} Returns `true` if a word is found, else `false`. + */ + function hasUnicodeWord(string) { + return reHasUnicodeWord.test(string); + } + + /** + * Converts `iterator` to an array. + * + * @private + * @param {Object} iterator The iterator to convert. + * @returns {Array} Returns the converted array. + */ + function iteratorToArray(iterator) { + var data, + result = []; + + while (!(data = iterator.next()).done) { + result.push(data.value); + } + return result; + } + + /** + * Converts `map` to its key-value pairs. + * + * @private + * @param {Object} map The map to convert. + * @returns {Array} Returns the key-value pairs. + */ + function mapToArray(map) { + var index = -1, + result = Array(map.size); + + map.forEach(function(value, key) { + result[++index] = [key, value]; + }); + return result; + } + + /** + * Creates a unary function that invokes `func` with its argument transformed. + * + * @private + * @param {Function} func The function to wrap. + * @param {Function} transform The argument transform. + * @returns {Function} Returns the new function. + */ + function overArg(func, transform) { + return function(arg) { + return func(transform(arg)); + }; + } + + /** + * Replaces all `placeholder` elements in `array` with an internal placeholder + * and returns an array of their indexes. + * + * @private + * @param {Array} array The array to modify. + * @param {*} placeholder The placeholder to replace. + * @returns {Array} Returns the new array of placeholder indexes. + */ + function replaceHolders(array, placeholder) { + var index = -1, + length = array.length, + resIndex = 0, + result = []; + + while (++index < length) { + var value = array[index]; + if (value === placeholder || value === PLACEHOLDER) { + array[index] = PLACEHOLDER; + result[resIndex++] = index; + } + } + return result; + } + + /** + * Converts `set` to an array of its values. + * + * @private + * @param {Object} set The set to convert. + * @returns {Array} Returns the values. + */ + function setToArray(set) { + var index = -1, + result = Array(set.size); + + set.forEach(function(value) { + result[++index] = value; + }); + return result; + } + + /** + * Converts `set` to its value-value pairs. + * + * @private + * @param {Object} set The set to convert. + * @returns {Array} Returns the value-value pairs. + */ + function setToPairs(set) { + var index = -1, + result = Array(set.size); + + set.forEach(function(value) { + result[++index] = [value, value]; + }); + return result; + } + + /** + * A specialized version of `_.indexOf` which performs strict equality + * comparisons of values, i.e. `===`. + * + * @private + * @param {Array} array The array to inspect. + * @param {*} value The value to search for. + * @param {number} fromIndex The index to search from. + * @returns {number} Returns the index of the matched value, else `-1`. + */ + function strictIndexOf(array, value, fromIndex) { + var index = fromIndex - 1, + length = array.length; + + while (++index < length) { + if (array[index] === value) { + return index; + } + } + return -1; + } + + /** + * A specialized version of `_.lastIndexOf` which performs strict equality + * comparisons of values, i.e. `===`. + * + * @private + * @param {Array} array The array to inspect. + * @param {*} value The value to search for. + * @param {number} fromIndex The index to search from. + * @returns {number} Returns the index of the matched value, else `-1`. + */ + function strictLastIndexOf(array, value, fromIndex) { + var index = fromIndex + 1; + while (index--) { + if (array[index] === value) { + return index; + } + } + return index; + } + + /** + * Gets the number of symbols in `string`. + * + * @private + * @param {string} string The string to inspect. + * @returns {number} Returns the string size. + */ + function stringSize(string) { + return hasUnicode(string) + ? unicodeSize(string) + : asciiSize(string); + } + + /** + * Converts `string` to an array. + * + * @private + * @param {string} string The string to convert. + * @returns {Array} Returns the converted array. + */ + function stringToArray(string) { + return hasUnicode(string) + ? unicodeToArray(string) + : asciiToArray(string); + } + + /** + * Used by `_.trim` and `_.trimEnd` to get the index of the last non-whitespace + * character of `string`. + * + * @private + * @param {string} string The string to inspect. + * @returns {number} Returns the index of the last non-whitespace character. + */ + function trimmedEndIndex(string) { + var index = string.length; + + while (index-- && reWhitespace.test(string.charAt(index))) {} + return index; + } + + /** + * Used by `_.unescape` to convert HTML entities to characters. + * + * @private + * @param {string} chr The matched character to unescape. + * @returns {string} Returns the unescaped character. + */ + var unescapeHtmlChar = basePropertyOf(htmlUnescapes); + + /** + * Gets the size of a Unicode `string`. + * + * @private + * @param {string} string The string inspect. + * @returns {number} Returns the string size. + */ + function unicodeSize(string) { + var result = reUnicode.lastIndex = 0; + while (reUnicode.test(string)) { + ++result; + } + return result; + } + + /** + * Converts a Unicode `string` to an array. + * + * @private + * @param {string} string The string to convert. + * @returns {Array} Returns the converted array. + */ + function unicodeToArray(string) { + return string.match(reUnicode) || []; + } + + /** + * Splits a Unicode `string` into an array of its words. + * + * @private + * @param {string} The string to inspect. + * @returns {Array} Returns the words of `string`. + */ + function unicodeWords(string) { + return string.match(reUnicodeWord) || []; + } + + /*--------------------------------------------------------------------------*/ + + /** + * Create a new pristine `lodash` function using the `context` object. + * + * @static + * @memberOf _ + * @since 1.1.0 + * @category Util + * @param {Object} [context=root] The context object. + * @returns {Function} Returns a new `lodash` function. + * @example + * + * _.mixin({ 'foo': _.constant('foo') }); + * + * var lodash = _.runInContext(); + * lodash.mixin({ 'bar': lodash.constant('bar') }); + * + * _.isFunction(_.foo); + * // => true + * _.isFunction(_.bar); + * // => false + * + * lodash.isFunction(lodash.foo); + * // => false + * lodash.isFunction(lodash.bar); + * // => true + * + * // Create a suped-up `defer` in Node.js. + * var defer = _.runInContext({ 'setTimeout': setImmediate }).defer; + */ + var runInContext = (function runInContext(context) { + context = context == null ? root : _.defaults(root.Object(), context, _.pick(root, contextProps)); + + /** Built-in constructor references. */ + var Array = context.Array, + Date = context.Date, + Error = context.Error, + Function = context.Function, + Math = context.Math, + Object = context.Object, + RegExp = context.RegExp, + String = context.String, + TypeError = context.TypeError; + + /** Used for built-in method references. */ + var arrayProto = Array.prototype, + funcProto = Function.prototype, + objectProto = Object.prototype; + + /** Used to detect overreaching core-js shims. */ + var coreJsData = context['__core-js_shared__']; + + /** Used to resolve the decompiled source of functions. */ + var funcToString = funcProto.toString; + + /** Used to check objects for own properties. */ + var hasOwnProperty = objectProto.hasOwnProperty; + + /** Used to generate unique IDs. */ + var idCounter = 0; + + /** Used to detect methods masquerading as native. */ + var maskSrcKey = (function() { + var uid = /[^.]+$/.exec(coreJsData && coreJsData.keys && coreJsData.keys.IE_PROTO || ''); + return uid ? ('Symbol(src)_1.' + uid) : ''; + }()); + + /** + * Used to resolve the + * [`toStringTag`](http://ecma-international.org/ecma-262/7.0/#sec-object.prototype.tostring) + * of values. + */ + var nativeObjectToString = objectProto.toString; + + /** Used to infer the `Object` constructor. */ + var objectCtorString = funcToString.call(Object); + + /** Used to restore the original `_` reference in `_.noConflict`. */ + var oldDash = root._; + + /** Used to detect if a method is native. */ + var reIsNative = RegExp('^' + + funcToString.call(hasOwnProperty).replace(reRegExpChar, '\\$&') + .replace(/hasOwnProperty|(function).*?(?=\\\()| for .+?(?=\\\])/g, '$1.*?') + '$' + ); + + /** Built-in value references. */ + var Buffer = moduleExports ? context.Buffer : undefined, + Symbol = context.Symbol, + Uint8Array = context.Uint8Array, + allocUnsafe = Buffer ? Buffer.allocUnsafe : undefined, + getPrototype = overArg(Object.getPrototypeOf, Object), + objectCreate = Object.create, + propertyIsEnumerable = objectProto.propertyIsEnumerable, + splice = arrayProto.splice, + spreadableSymbol = Symbol ? Symbol.isConcatSpreadable : undefined, + symIterator = Symbol ? Symbol.iterator : undefined, + symToStringTag = Symbol ? Symbol.toStringTag : undefined; + + var defineProperty = (function() { + try { + var func = getNative(Object, 'defineProperty'); + func({}, '', {}); + return func; + } catch (e) {} + }()); + + /** Mocked built-ins. */ + var ctxClearTimeout = context.clearTimeout !== root.clearTimeout && context.clearTimeout, + ctxNow = Date && Date.now !== root.Date.now && Date.now, + ctxSetTimeout = context.setTimeout !== root.setTimeout && context.setTimeout; + + /* Built-in method references for those with the same name as other `lodash` methods. */ + var nativeCeil = Math.ceil, + nativeFloor = Math.floor, + nativeGetSymbols = Object.getOwnPropertySymbols, + nativeIsBuffer = Buffer ? Buffer.isBuffer : undefined, + nativeIsFinite = context.isFinite, + nativeJoin = arrayProto.join, + nativeKeys = overArg(Object.keys, Object), + nativeMax = Math.max, + nativeMin = Math.min, + nativeNow = Date.now, + nativeParseInt = context.parseInt, + nativeRandom = Math.random, + nativeReverse = arrayProto.reverse; + + /* Built-in method references that are verified to be native. */ + var DataView = getNative(context, 'DataView'), + Map = getNative(context, 'Map'), + Promise = getNative(context, 'Promise'), + Set = getNative(context, 'Set'), + WeakMap = getNative(context, 'WeakMap'), + nativeCreate = getNative(Object, 'create'); + + /** Used to store function metadata. */ + var metaMap = WeakMap && new WeakMap; + + /** Used to lookup unminified function names. */ + var realNames = {}; + + /** Used to detect maps, sets, and weakmaps. */ + var dataViewCtorString = toSource(DataView), + mapCtorString = toSource(Map), + promiseCtorString = toSource(Promise), + setCtorString = toSource(Set), + weakMapCtorString = toSource(WeakMap); + + /** Used to convert symbols to primitives and strings. */ + var symbolProto = Symbol ? Symbol.prototype : undefined, + symbolValueOf = symbolProto ? symbolProto.valueOf : undefined, + symbolToString = symbolProto ? symbolProto.toString : undefined; + + /*------------------------------------------------------------------------*/ + + /** + * Creates a `lodash` object which wraps `value` to enable implicit method + * chain sequences. Methods that operate on and return arrays, collections, + * and functions can be chained together. Methods that retrieve a single value + * or may return a primitive value will automatically end the chain sequence + * and return the unwrapped value. Otherwise, the value must be unwrapped + * with `_#value`. + * + * Explicit chain sequences, which must be unwrapped with `_#value`, may be + * enabled using `_.chain`. + * + * The execution of chained methods is lazy, that is, it's deferred until + * `_#value` is implicitly or explicitly called. + * + * Lazy evaluation allows several methods to support shortcut fusion. + * Shortcut fusion is an optimization to merge iteratee calls; this avoids + * the creation of intermediate arrays and can greatly reduce the number of + * iteratee executions. Sections of a chain sequence qualify for shortcut + * fusion if the section is applied to an array and iteratees accept only + * one argument. The heuristic for whether a section qualifies for shortcut + * fusion is subject to change. + * + * Chaining is supported in custom builds as long as the `_#value` method is + * directly or indirectly included in the build. + * + * In addition to lodash methods, wrappers have `Array` and `String` methods. + * + * The wrapper `Array` methods are: + * `concat`, `join`, `pop`, `push`, `shift`, `sort`, `splice`, and `unshift` + * + * The wrapper `String` methods are: + * `replace` and `split` + * + * The wrapper methods that support shortcut fusion are: + * `at`, `compact`, `drop`, `dropRight`, `dropWhile`, `filter`, `find`, + * `findLast`, `head`, `initial`, `last`, `map`, `reject`, `reverse`, `slice`, + * `tail`, `take`, `takeRight`, `takeRightWhile`, `takeWhile`, and `toArray` + * + * The chainable wrapper methods are: + * `after`, `ary`, `assign`, `assignIn`, `assignInWith`, `assignWith`, `at`, + * `before`, `bind`, `bindAll`, `bindKey`, `castArray`, `chain`, `chunk`, + * `commit`, `compact`, `concat`, `conforms`, `constant`, `countBy`, `create`, + * `curry`, `debounce`, `defaults`, `defaultsDeep`, `defer`, `delay`, + * `difference`, `differenceBy`, `differenceWith`, `drop`, `dropRight`, + * `dropRightWhile`, `dropWhile`, `extend`, `extendWith`, `fill`, `filter`, + * `flatMap`, `flatMapDeep`, `flatMapDepth`, `flatten`, `flattenDeep`, + * `flattenDepth`, `flip`, `flow`, `flowRight`, `fromPairs`, `functions`, + * `functionsIn`, `groupBy`, `initial`, `intersection`, `intersectionBy`, + * `intersectionWith`, `invert`, `invertBy`, `invokeMap`, `iteratee`, `keyBy`, + * `keys`, `keysIn`, `map`, `mapKeys`, `mapValues`, `matches`, `matchesProperty`, + * `memoize`, `merge`, `mergeWith`, `method`, `methodOf`, `mixin`, `negate`, + * `nthArg`, `omit`, `omitBy`, `once`, `orderBy`, `over`, `overArgs`, + * `overEvery`, `overSome`, `partial`, `partialRight`, `partition`, `pick`, + * `pickBy`, `plant`, `property`, `propertyOf`, `pull`, `pullAll`, `pullAllBy`, + * `pullAllWith`, `pullAt`, `push`, `range`, `rangeRight`, `rearg`, `reject`, + * `remove`, `rest`, `reverse`, `sampleSize`, `set`, `setWith`, `shuffle`, + * `slice`, `sort`, `sortBy`, `splice`, `spread`, `tail`, `take`, `takeRight`, + * `takeRightWhile`, `takeWhile`, `tap`, `throttle`, `thru`, `toArray`, + * `toPairs`, `toPairsIn`, `toPath`, `toPlainObject`, `transform`, `unary`, + * `union`, `unionBy`, `unionWith`, `uniq`, `uniqBy`, `uniqWith`, `unset`, + * `unshift`, `unzip`, `unzipWith`, `update`, `updateWith`, `values`, + * `valuesIn`, `without`, `wrap`, `xor`, `xorBy`, `xorWith`, `zip`, + * `zipObject`, `zipObjectDeep`, and `zipWith` + * + * The wrapper methods that are **not** chainable by default are: + * `add`, `attempt`, `camelCase`, `capitalize`, `ceil`, `clamp`, `clone`, + * `cloneDeep`, `cloneDeepWith`, `cloneWith`, `conformsTo`, `deburr`, + * `defaultTo`, `divide`, `each`, `eachRight`, `endsWith`, `eq`, `escape`, + * `escapeRegExp`, `every`, `find`, `findIndex`, `findKey`, `findLast`, + * `findLastIndex`, `findLastKey`, `first`, `floor`, `forEach`, `forEachRight`, + * `forIn`, `forInRight`, `forOwn`, `forOwnRight`, `get`, `gt`, `gte`, `has`, + * `hasIn`, `head`, `identity`, `includes`, `indexOf`, `inRange`, `invoke`, + * `isArguments`, `isArray`, `isArrayBuffer`, `isArrayLike`, `isArrayLikeObject`, + * `isBoolean`, `isBuffer`, `isDate`, `isElement`, `isEmpty`, `isEqual`, + * `isEqualWith`, `isError`, `isFinite`, `isFunction`, `isInteger`, `isLength`, + * `isMap`, `isMatch`, `isMatchWith`, `isNaN`, `isNative`, `isNil`, `isNull`, + * `isNumber`, `isObject`, `isObjectLike`, `isPlainObject`, `isRegExp`, + * `isSafeInteger`, `isSet`, `isString`, `isUndefined`, `isTypedArray`, + * `isWeakMap`, `isWeakSet`, `join`, `kebabCase`, `last`, `lastIndexOf`, + * `lowerCase`, `lowerFirst`, `lt`, `lte`, `max`, `maxBy`, `mean`, `meanBy`, + * `min`, `minBy`, `multiply`, `noConflict`, `noop`, `now`, `nth`, `pad`, + * `padEnd`, `padStart`, `parseInt`, `pop`, `random`, `reduce`, `reduceRight`, + * `repeat`, `result`, `round`, `runInContext`, `sample`, `shift`, `size`, + * `snakeCase`, `some`, `sortedIndex`, `sortedIndexBy`, `sortedLastIndex`, + * `sortedLastIndexBy`, `startCase`, `startsWith`, `stubArray`, `stubFalse`, + * `stubObject`, `stubString`, `stubTrue`, `subtract`, `sum`, `sumBy`, + * `template`, `times`, `toFinite`, `toInteger`, `toJSON`, `toLength`, + * `toLower`, `toNumber`, `toSafeInteger`, `toString`, `toUpper`, `trim`, + * `trimEnd`, `trimStart`, `truncate`, `unescape`, `uniqueId`, `upperCase`, + * `upperFirst`, `value`, and `words` + * + * @name _ + * @constructor + * @category Seq + * @param {*} value The value to wrap in a `lodash` instance. + * @returns {Object} Returns the new `lodash` wrapper instance. + * @example + * + * function square(n) { + * return n * n; + * } + * + * var wrapped = _([1, 2, 3]); + * + * // Returns an unwrapped value. + * wrapped.reduce(_.add); + * // => 6 + * + * // Returns a wrapped value. + * var squares = wrapped.map(square); + * + * _.isArray(squares); + * // => false + * + * _.isArray(squares.value()); + * // => true + */ + function lodash(value) { + if (isObjectLike(value) && !isArray(value) && !(value instanceof LazyWrapper)) { + if (value instanceof LodashWrapper) { + return value; + } + if (hasOwnProperty.call(value, '__wrapped__')) { + return wrapperClone(value); + } + } + return new LodashWrapper(value); + } + + /** + * The base implementation of `_.create` without support for assigning + * properties to the created object. + * + * @private + * @param {Object} proto The object to inherit from. + * @returns {Object} Returns the new object. + */ + var baseCreate = (function() { + function object() {} + return function(proto) { + if (!isObject(proto)) { + return {}; + } + if (objectCreate) { + return objectCreate(proto); + } + object.prototype = proto; + var result = new object; + object.prototype = undefined; + return result; + }; + }()); + + /** + * The function whose prototype chain sequence wrappers inherit from. + * + * @private + */ + function baseLodash() { + // No operation performed. + } + + /** + * The base constructor for creating `lodash` wrapper objects. + * + * @private + * @param {*} value The value to wrap. + * @param {boolean} [chainAll] Enable explicit method chain sequences. + */ + function LodashWrapper(value, chainAll) { + this.__wrapped__ = value; + this.__actions__ = []; + this.__chain__ = !!chainAll; + this.__index__ = 0; + this.__values__ = undefined; + } + + /** + * By default, the template delimiters used by lodash are like those in + * embedded Ruby (ERB) as well as ES2015 template strings. Change the + * following template settings to use alternative delimiters. + * + * @static + * @memberOf _ + * @type {Object} + */ + lodash.templateSettings = { + + /** + * Used to detect `data` property values to be HTML-escaped. + * + * @memberOf _.templateSettings + * @type {RegExp} + */ + 'escape': reEscape, + + /** + * Used to detect code to be evaluated. + * + * @memberOf _.templateSettings + * @type {RegExp} + */ + 'evaluate': reEvaluate, + + /** + * Used to detect `data` property values to inject. + * + * @memberOf _.templateSettings + * @type {RegExp} + */ + 'interpolate': reInterpolate, + + /** + * Used to reference the data object in the template text. + * + * @memberOf _.templateSettings + * @type {string} + */ + 'variable': '', + + /** + * Used to import variables into the compiled template. + * + * @memberOf _.templateSettings + * @type {Object} + */ + 'imports': { + + /** + * A reference to the `lodash` function. + * + * @memberOf _.templateSettings.imports + * @type {Function} + */ + '_': lodash + } + }; + + // Ensure wrappers are instances of `baseLodash`. + lodash.prototype = baseLodash.prototype; + lodash.prototype.constructor = lodash; + + LodashWrapper.prototype = baseCreate(baseLodash.prototype); + LodashWrapper.prototype.constructor = LodashWrapper; + + /*------------------------------------------------------------------------*/ + + /** + * Creates a lazy wrapper object which wraps `value` to enable lazy evaluation. + * + * @private + * @constructor + * @param {*} value The value to wrap. + */ + function LazyWrapper(value) { + this.__wrapped__ = value; + this.__actions__ = []; + this.__dir__ = 1; + this.__filtered__ = false; + this.__iteratees__ = []; + this.__takeCount__ = MAX_ARRAY_LENGTH; + this.__views__ = []; + } + + /** + * Creates a clone of the lazy wrapper object. + * + * @private + * @name clone + * @memberOf LazyWrapper + * @returns {Object} Returns the cloned `LazyWrapper` object. + */ + function lazyClone() { + var result = new LazyWrapper(this.__wrapped__); + result.__actions__ = copyArray(this.__actions__); + result.__dir__ = this.__dir__; + result.__filtered__ = this.__filtered__; + result.__iteratees__ = copyArray(this.__iteratees__); + result.__takeCount__ = this.__takeCount__; + result.__views__ = copyArray(this.__views__); + return result; + } + + /** + * Reverses the direction of lazy iteration. + * + * @private + * @name reverse + * @memberOf LazyWrapper + * @returns {Object} Returns the new reversed `LazyWrapper` object. + */ + function lazyReverse() { + if (this.__filtered__) { + var result = new LazyWrapper(this); + result.__dir__ = -1; + result.__filtered__ = true; + } else { + result = this.clone(); + result.__dir__ *= -1; + } + return result; + } + + /** + * Extracts the unwrapped value from its lazy wrapper. + * + * @private + * @name value + * @memberOf LazyWrapper + * @returns {*} Returns the unwrapped value. + */ + function lazyValue() { + var array = this.__wrapped__.value(), + dir = this.__dir__, + isArr = isArray(array), + isRight = dir < 0, + arrLength = isArr ? array.length : 0, + view = getView(0, arrLength, this.__views__), + start = view.start, + end = view.end, + length = end - start, + index = isRight ? end : (start - 1), + iteratees = this.__iteratees__, + iterLength = iteratees.length, + resIndex = 0, + takeCount = nativeMin(length, this.__takeCount__); + + if (!isArr || (!isRight && arrLength == length && takeCount == length)) { + return baseWrapperValue(array, this.__actions__); + } + var result = []; + + outer: + while (length-- && resIndex < takeCount) { + index += dir; + + var iterIndex = -1, + value = array[index]; + + while (++iterIndex < iterLength) { + var data = iteratees[iterIndex], + iteratee = data.iteratee, + type = data.type, + computed = iteratee(value); + + if (type == LAZY_MAP_FLAG) { + value = computed; + } else if (!computed) { + if (type == LAZY_FILTER_FLAG) { + continue outer; + } else { + break outer; + } + } + } + result[resIndex++] = value; + } + return result; + } + + // Ensure `LazyWrapper` is an instance of `baseLodash`. + LazyWrapper.prototype = baseCreate(baseLodash.prototype); + LazyWrapper.prototype.constructor = LazyWrapper; + + /*------------------------------------------------------------------------*/ + + /** + * Creates a hash object. + * + * @private + * @constructor + * @param {Array} [entries] The key-value pairs to cache. + */ + function Hash(entries) { + var index = -1, + length = entries == null ? 0 : entries.length; + + this.clear(); + while (++index < length) { + var entry = entries[index]; + this.set(entry[0], entry[1]); + } + } + + /** + * Removes all key-value entries from the hash. + * + * @private + * @name clear + * @memberOf Hash + */ + function hashClear() { + this.__data__ = nativeCreate ? nativeCreate(null) : {}; + this.size = 0; + } + + /** + * Removes `key` and its value from the hash. + * + * @private + * @name delete + * @memberOf Hash + * @param {Object} hash The hash to modify. + * @param {string} key The key of the value to remove. + * @returns {boolean} Returns `true` if the entry was removed, else `false`. + */ + function hashDelete(key) { + var result = this.has(key) && delete this.__data__[key]; + this.size -= result ? 1 : 0; + return result; + } + + /** + * Gets the hash value for `key`. + * + * @private + * @name get + * @memberOf Hash + * @param {string} key The key of the value to get. + * @returns {*} Returns the entry value. + */ + function hashGet(key) { + var data = this.__data__; + if (nativeCreate) { + var result = data[key]; + return result === HASH_UNDEFINED ? undefined : result; + } + return hasOwnProperty.call(data, key) ? data[key] : undefined; + } + + /** + * Checks if a hash value for `key` exists. + * + * @private + * @name has + * @memberOf Hash + * @param {string} key The key of the entry to check. + * @returns {boolean} Returns `true` if an entry for `key` exists, else `false`. + */ + function hashHas(key) { + var data = this.__data__; + return nativeCreate ? (data[key] !== undefined) : hasOwnProperty.call(data, key); + } + + /** + * Sets the hash `key` to `value`. + * + * @private + * @name set + * @memberOf Hash + * @param {string} key The key of the value to set. + * @param {*} value The value to set. + * @returns {Object} Returns the hash instance. + */ + function hashSet(key, value) { + var data = this.__data__; + this.size += this.has(key) ? 0 : 1; + data[key] = (nativeCreate && value === undefined) ? HASH_UNDEFINED : value; + return this; + } + + // Add methods to `Hash`. + Hash.prototype.clear = hashClear; + Hash.prototype['delete'] = hashDelete; + Hash.prototype.get = hashGet; + Hash.prototype.has = hashHas; + Hash.prototype.set = hashSet; + + /*------------------------------------------------------------------------*/ + + /** + * Creates an list cache object. + * + * @private + * @constructor + * @param {Array} [entries] The key-value pairs to cache. + */ + function ListCache(entries) { + var index = -1, + length = entries == null ? 0 : entries.length; + + this.clear(); + while (++index < length) { + var entry = entries[index]; + this.set(entry[0], entry[1]); + } + } + + /** + * Removes all key-value entries from the list cache. + * + * @private + * @name clear + * @memberOf ListCache + */ + function listCacheClear() { + this.__data__ = []; + this.size = 0; + } + + /** + * Removes `key` and its value from the list cache. + * + * @private + * @name delete + * @memberOf ListCache + * @param {string} key The key of the value to remove. + * @returns {boolean} Returns `true` if the entry was removed, else `false`. + */ + function listCacheDelete(key) { + var data = this.__data__, + index = assocIndexOf(data, key); + + if (index < 0) { + return false; + } + var lastIndex = data.length - 1; + if (index == lastIndex) { + data.pop(); + } else { + splice.call(data, index, 1); + } + --this.size; + return true; + } + + /** + * Gets the list cache value for `key`. + * + * @private + * @name get + * @memberOf ListCache + * @param {string} key The key of the value to get. + * @returns {*} Returns the entry value. + */ + function listCacheGet(key) { + var data = this.__data__, + index = assocIndexOf(data, key); + + return index < 0 ? undefined : data[index][1]; + } + + /** + * Checks if a list cache value for `key` exists. + * + * @private + * @name has + * @memberOf ListCache + * @param {string} key The key of the entry to check. + * @returns {boolean} Returns `true` if an entry for `key` exists, else `false`. + */ + function listCacheHas(key) { + return assocIndexOf(this.__data__, key) > -1; + } + + /** + * Sets the list cache `key` to `value`. + * + * @private + * @name set + * @memberOf ListCache + * @param {string} key The key of the value to set. + * @param {*} value The value to set. + * @returns {Object} Returns the list cache instance. + */ + function listCacheSet(key, value) { + var data = this.__data__, + index = assocIndexOf(data, key); + + if (index < 0) { + ++this.size; + data.push([key, value]); + } else { + data[index][1] = value; + } + return this; + } + + // Add methods to `ListCache`. + ListCache.prototype.clear = listCacheClear; + ListCache.prototype['delete'] = listCacheDelete; + ListCache.prototype.get = listCacheGet; + ListCache.prototype.has = listCacheHas; + ListCache.prototype.set = listCacheSet; + + /*------------------------------------------------------------------------*/ + + /** + * Creates a map cache object to store key-value pairs. + * + * @private + * @constructor + * @param {Array} [entries] The key-value pairs to cache. + */ + function MapCache(entries) { + var index = -1, + length = entries == null ? 0 : entries.length; + + this.clear(); + while (++index < length) { + var entry = entries[index]; + this.set(entry[0], entry[1]); + } + } + + /** + * Removes all key-value entries from the map. + * + * @private + * @name clear + * @memberOf MapCache + */ + function mapCacheClear() { + this.size = 0; + this.__data__ = { + 'hash': new Hash, + 'map': new (Map || ListCache), + 'string': new Hash + }; + } + + /** + * Removes `key` and its value from the map. + * + * @private + * @name delete + * @memberOf MapCache + * @param {string} key The key of the value to remove. + * @returns {boolean} Returns `true` if the entry was removed, else `false`. + */ + function mapCacheDelete(key) { + var result = getMapData(this, key)['delete'](key); + this.size -= result ? 1 : 0; + return result; + } + + /** + * Gets the map value for `key`. + * + * @private + * @name get + * @memberOf MapCache + * @param {string} key The key of the value to get. + * @returns {*} Returns the entry value. + */ + function mapCacheGet(key) { + return getMapData(this, key).get(key); + } + + /** + * Checks if a map value for `key` exists. + * + * @private + * @name has + * @memberOf MapCache + * @param {string} key The key of the entry to check. + * @returns {boolean} Returns `true` if an entry for `key` exists, else `false`. + */ + function mapCacheHas(key) { + return getMapData(this, key).has(key); + } + + /** + * Sets the map `key` to `value`. + * + * @private + * @name set + * @memberOf MapCache + * @param {string} key The key of the value to set. + * @param {*} value The value to set. + * @returns {Object} Returns the map cache instance. + */ + function mapCacheSet(key, value) { + var data = getMapData(this, key), + size = data.size; + + data.set(key, value); + this.size += data.size == size ? 0 : 1; + return this; + } + + // Add methods to `MapCache`. + MapCache.prototype.clear = mapCacheClear; + MapCache.prototype['delete'] = mapCacheDelete; + MapCache.prototype.get = mapCacheGet; + MapCache.prototype.has = mapCacheHas; + MapCache.prototype.set = mapCacheSet; + + /*------------------------------------------------------------------------*/ + + /** + * + * Creates an array cache object to store unique values. + * + * @private + * @constructor + * @param {Array} [values] The values to cache. + */ + function SetCache(values) { + var index = -1, + length = values == null ? 0 : values.length; + + this.__data__ = new MapCache; + while (++index < length) { + this.add(values[index]); + } + } + + /** + * Adds `value` to the array cache. + * + * @private + * @name add + * @memberOf SetCache + * @alias push + * @param {*} value The value to cache. + * @returns {Object} Returns the cache instance. + */ + function setCacheAdd(value) { + this.__data__.set(value, HASH_UNDEFINED); + return this; + } + + /** + * Checks if `value` is in the array cache. + * + * @private + * @name has + * @memberOf SetCache + * @param {*} value The value to search for. + * @returns {number} Returns `true` if `value` is found, else `false`. + */ + function setCacheHas(value) { + return this.__data__.has(value); + } + + // Add methods to `SetCache`. + SetCache.prototype.add = SetCache.prototype.push = setCacheAdd; + SetCache.prototype.has = setCacheHas; + + /*------------------------------------------------------------------------*/ + + /** + * Creates a stack cache object to store key-value pairs. + * + * @private + * @constructor + * @param {Array} [entries] The key-value pairs to cache. + */ + function Stack(entries) { + var data = this.__data__ = new ListCache(entries); + this.size = data.size; + } + + /** + * Removes all key-value entries from the stack. + * + * @private + * @name clear + * @memberOf Stack + */ + function stackClear() { + this.__data__ = new ListCache; + this.size = 0; + } + + /** + * Removes `key` and its value from the stack. + * + * @private + * @name delete + * @memberOf Stack + * @param {string} key The key of the value to remove. + * @returns {boolean} Returns `true` if the entry was removed, else `false`. + */ + function stackDelete(key) { + var data = this.__data__, + result = data['delete'](key); + + this.size = data.size; + return result; + } + + /** + * Gets the stack value for `key`. + * + * @private + * @name get + * @memberOf Stack + * @param {string} key The key of the value to get. + * @returns {*} Returns the entry value. + */ + function stackGet(key) { + return this.__data__.get(key); + } + + /** + * Checks if a stack value for `key` exists. + * + * @private + * @name has + * @memberOf Stack + * @param {string} key The key of the entry to check. + * @returns {boolean} Returns `true` if an entry for `key` exists, else `false`. + */ + function stackHas(key) { + return this.__data__.has(key); + } + + /** + * Sets the stack `key` to `value`. + * + * @private + * @name set + * @memberOf Stack + * @param {string} key The key of the value to set. + * @param {*} value The value to set. + * @returns {Object} Returns the stack cache instance. + */ + function stackSet(key, value) { + var data = this.__data__; + if (data instanceof ListCache) { + var pairs = data.__data__; + if (!Map || (pairs.length < LARGE_ARRAY_SIZE - 1)) { + pairs.push([key, value]); + this.size = ++data.size; + return this; + } + data = this.__data__ = new MapCache(pairs); + } + data.set(key, value); + this.size = data.size; + return this; + } + + // Add methods to `Stack`. + Stack.prototype.clear = stackClear; + Stack.prototype['delete'] = stackDelete; + Stack.prototype.get = stackGet; + Stack.prototype.has = stackHas; + Stack.prototype.set = stackSet; + + /*------------------------------------------------------------------------*/ + + /** + * Creates an array of the enumerable property names of the array-like `value`. + * + * @private + * @param {*} value The value to query. + * @param {boolean} inherited Specify returning inherited property names. + * @returns {Array} Returns the array of property names. + */ + function arrayLikeKeys(value, inherited) { + var isArr = isArray(value), + isArg = !isArr && isArguments(value), + isBuff = !isArr && !isArg && isBuffer(value), + isType = !isArr && !isArg && !isBuff && isTypedArray(value), + skipIndexes = isArr || isArg || isBuff || isType, + result = skipIndexes ? baseTimes(value.length, String) : [], + length = result.length; + + for (var key in value) { + if ((inherited || hasOwnProperty.call(value, key)) && + !(skipIndexes && ( + // Safari 9 has enumerable `arguments.length` in strict mode. + key == 'length' || + // Node.js 0.10 has enumerable non-index properties on buffers. + (isBuff && (key == 'offset' || key == 'parent')) || + // PhantomJS 2 has enumerable non-index properties on typed arrays. + (isType && (key == 'buffer' || key == 'byteLength' || key == 'byteOffset')) || + // Skip index properties. + isIndex(key, length) + ))) { + result.push(key); + } + } + return result; + } + + /** + * A specialized version of `_.sample` for arrays. + * + * @private + * @param {Array} array The array to sample. + * @returns {*} Returns the random element. + */ + function arraySample(array) { + var length = array.length; + return length ? array[baseRandom(0, length - 1)] : undefined; + } + + /** + * A specialized version of `_.sampleSize` for arrays. + * + * @private + * @param {Array} array The array to sample. + * @param {number} n The number of elements to sample. + * @returns {Array} Returns the random elements. + */ + function arraySampleSize(array, n) { + return shuffleSelf(copyArray(array), baseClamp(n, 0, array.length)); + } + + /** + * A specialized version of `_.shuffle` for arrays. + * + * @private + * @param {Array} array The array to shuffle. + * @returns {Array} Returns the new shuffled array. + */ + function arrayShuffle(array) { + return shuffleSelf(copyArray(array)); + } + + /** + * This function is like `assignValue` except that it doesn't assign + * `undefined` values. + * + * @private + * @param {Object} object The object to modify. + * @param {string} key The key of the property to assign. + * @param {*} value The value to assign. + */ + function assignMergeValue(object, key, value) { + if ((value !== undefined && !eq(object[key], value)) || + (value === undefined && !(key in object))) { + baseAssignValue(object, key, value); + } + } + + /** + * Assigns `value` to `key` of `object` if the existing value is not equivalent + * using [`SameValueZero`](http://ecma-international.org/ecma-262/7.0/#sec-samevaluezero) + * for equality comparisons. + * + * @private + * @param {Object} object The object to modify. + * @param {string} key The key of the property to assign. + * @param {*} value The value to assign. + */ + function assignValue(object, key, value) { + var objValue = object[key]; + if (!(hasOwnProperty.call(object, key) && eq(objValue, value)) || + (value === undefined && !(key in object))) { + baseAssignValue(object, key, value); + } + } + + /** + * Gets the index at which the `key` is found in `array` of key-value pairs. + * + * @private + * @param {Array} array The array to inspect. + * @param {*} key The key to search for. + * @returns {number} Returns the index of the matched value, else `-1`. + */ + function assocIndexOf(array, key) { + var length = array.length; + while (length--) { + if (eq(array[length][0], key)) { + return length; + } + } + return -1; + } + + /** + * Aggregates elements of `collection` on `accumulator` with keys transformed + * by `iteratee` and values set by `setter`. + * + * @private + * @param {Array|Object} collection The collection to iterate over. + * @param {Function} setter The function to set `accumulator` values. + * @param {Function} iteratee The iteratee to transform keys. + * @param {Object} accumulator The initial aggregated object. + * @returns {Function} Returns `accumulator`. + */ + function baseAggregator(collection, setter, iteratee, accumulator) { + baseEach(collection, function(value, key, collection) { + setter(accumulator, value, iteratee(value), collection); + }); + return accumulator; + } + + /** + * The base implementation of `_.assign` without support for multiple sources + * or `customizer` functions. + * + * @private + * @param {Object} object The destination object. + * @param {Object} source The source object. + * @returns {Object} Returns `object`. + */ + function baseAssign(object, source) { + return object && copyObject(source, keys(source), object); + } + + /** + * The base implementation of `_.assignIn` without support for multiple sources + * or `customizer` functions. + * + * @private + * @param {Object} object The destination object. + * @param {Object} source The source object. + * @returns {Object} Returns `object`. + */ + function baseAssignIn(object, source) { + return object && copyObject(source, keysIn(source), object); + } + + /** + * The base implementation of `assignValue` and `assignMergeValue` without + * value checks. + * + * @private + * @param {Object} object The object to modify. + * @param {string} key The key of the property to assign. + * @param {*} value The value to assign. + */ + function baseAssignValue(object, key, value) { + if (key == '__proto__' && defineProperty) { + defineProperty(object, key, { + 'configurable': true, + 'enumerable': true, + 'value': value, + 'writable': true + }); + } else { + object[key] = value; + } + } + + /** + * The base implementation of `_.at` without support for individual paths. + * + * @private + * @param {Object} object The object to iterate over. + * @param {string[]} paths The property paths to pick. + * @returns {Array} Returns the picked elements. + */ + function baseAt(object, paths) { + var index = -1, + length = paths.length, + result = Array(length), + skip = object == null; + + while (++index < length) { + result[index] = skip ? undefined : get(object, paths[index]); + } + return result; + } + + /** + * The base implementation of `_.clamp` which doesn't coerce arguments. + * + * @private + * @param {number} number The number to clamp. + * @param {number} [lower] The lower bound. + * @param {number} upper The upper bound. + * @returns {number} Returns the clamped number. + */ + function baseClamp(number, lower, upper) { + if (number === number) { + if (upper !== undefined) { + number = number <= upper ? number : upper; + } + if (lower !== undefined) { + number = number >= lower ? number : lower; + } + } + return number; + } + + /** + * The base implementation of `_.clone` and `_.cloneDeep` which tracks + * traversed objects. + * + * @private + * @param {*} value The value to clone. + * @param {boolean} bitmask The bitmask flags. + * 1 - Deep clone + * 2 - Flatten inherited properties + * 4 - Clone symbols + * @param {Function} [customizer] The function to customize cloning. + * @param {string} [key] The key of `value`. + * @param {Object} [object] The parent object of `value`. + * @param {Object} [stack] Tracks traversed objects and their clone counterparts. + * @returns {*} Returns the cloned value. + */ + function baseClone(value, bitmask, customizer, key, object, stack) { + var result, + isDeep = bitmask & CLONE_DEEP_FLAG, + isFlat = bitmask & CLONE_FLAT_FLAG, + isFull = bitmask & CLONE_SYMBOLS_FLAG; + + if (customizer) { + result = object ? customizer(value, key, object, stack) : customizer(value); + } + if (result !== undefined) { + return result; + } + if (!isObject(value)) { + return value; + } + var isArr = isArray(value); + if (isArr) { + result = initCloneArray(value); + if (!isDeep) { + return copyArray(value, result); + } + } else { + var tag = getTag(value), + isFunc = tag == funcTag || tag == genTag; + + if (isBuffer(value)) { + return cloneBuffer(value, isDeep); + } + if (tag == objectTag || tag == argsTag || (isFunc && !object)) { + result = (isFlat || isFunc) ? {} : initCloneObject(value); + if (!isDeep) { + return isFlat + ? copySymbolsIn(value, baseAssignIn(result, value)) + : copySymbols(value, baseAssign(result, value)); + } + } else { + if (!cloneableTags[tag]) { + return object ? value : {}; + } + result = initCloneByTag(value, tag, isDeep); + } + } + // Check for circular references and return its corresponding clone. + stack || (stack = new Stack); + var stacked = stack.get(value); + if (stacked) { + return stacked; + } + stack.set(value, result); + + if (isSet(value)) { + value.forEach(function(subValue) { + result.add(baseClone(subValue, bitmask, customizer, subValue, value, stack)); + }); + } else if (isMap(value)) { + value.forEach(function(subValue, key) { + result.set(key, baseClone(subValue, bitmask, customizer, key, value, stack)); + }); + } + + var keysFunc = isFull + ? (isFlat ? getAllKeysIn : getAllKeys) + : (isFlat ? keysIn : keys); + + var props = isArr ? undefined : keysFunc(value); + arrayEach(props || value, function(subValue, key) { + if (props) { + key = subValue; + subValue = value[key]; + } + // Recursively populate clone (susceptible to call stack limits). + assignValue(result, key, baseClone(subValue, bitmask, customizer, key, value, stack)); + }); + return result; + } + + /** + * The base implementation of `_.conforms` which doesn't clone `source`. + * + * @private + * @param {Object} source The object of property predicates to conform to. + * @returns {Function} Returns the new spec function. + */ + function baseConforms(source) { + var props = keys(source); + return function(object) { + return baseConformsTo(object, source, props); + }; + } + + /** + * The base implementation of `_.conformsTo` which accepts `props` to check. + * + * @private + * @param {Object} object The object to inspect. + * @param {Object} source The object of property predicates to conform to. + * @returns {boolean} Returns `true` if `object` conforms, else `false`. + */ + function baseConformsTo(object, source, props) { + var length = props.length; + if (object == null) { + return !length; + } + object = Object(object); + while (length--) { + var key = props[length], + predicate = source[key], + value = object[key]; + + if ((value === undefined && !(key in object)) || !predicate(value)) { + return false; + } + } + return true; + } + + /** + * The base implementation of `_.delay` and `_.defer` which accepts `args` + * to provide to `func`. + * + * @private + * @param {Function} func The function to delay. + * @param {number} wait The number of milliseconds to delay invocation. + * @param {Array} args The arguments to provide to `func`. + * @returns {number|Object} Returns the timer id or timeout object. + */ + function baseDelay(func, wait, args) { + if (typeof func != 'function') { + throw new TypeError(FUNC_ERROR_TEXT); + } + return setTimeout(function() { func.apply(undefined, args); }, wait); + } + + /** + * The base implementation of methods like `_.difference` without support + * for excluding multiple arrays or iteratee shorthands. + * + * @private + * @param {Array} array The array to inspect. + * @param {Array} values The values to exclude. + * @param {Function} [iteratee] The iteratee invoked per element. + * @param {Function} [comparator] The comparator invoked per element. + * @returns {Array} Returns the new array of filtered values. + */ + function baseDifference(array, values, iteratee, comparator) { + var index = -1, + includes = arrayIncludes, + isCommon = true, + length = array.length, + result = [], + valuesLength = values.length; + + if (!length) { + return result; + } + if (iteratee) { + values = arrayMap(values, baseUnary(iteratee)); + } + if (comparator) { + includes = arrayIncludesWith; + isCommon = false; + } + else if (values.length >= LARGE_ARRAY_SIZE) { + includes = cacheHas; + isCommon = false; + values = new SetCache(values); + } + outer: + while (++index < length) { + var value = array[index], + computed = iteratee == null ? value : iteratee(value); + + value = (comparator || value !== 0) ? value : 0; + if (isCommon && computed === computed) { + var valuesIndex = valuesLength; + while (valuesIndex--) { + if (values[valuesIndex] === computed) { + continue outer; + } + } + result.push(value); + } + else if (!includes(values, computed, comparator)) { + result.push(value); + } + } + return result; + } + + /** + * The base implementation of `_.forEach` without support for iteratee shorthands. + * + * @private + * @param {Array|Object} collection The collection to iterate over. + * @param {Function} iteratee The function invoked per iteration. + * @returns {Array|Object} Returns `collection`. + */ + var baseEach = createBaseEach(baseForOwn); + + /** + * The base implementation of `_.forEachRight` without support for iteratee shorthands. + * + * @private + * @param {Array|Object} collection The collection to iterate over. + * @param {Function} iteratee The function invoked per iteration. + * @returns {Array|Object} Returns `collection`. + */ + var baseEachRight = createBaseEach(baseForOwnRight, true); + + /** + * The base implementation of `_.every` without support for iteratee shorthands. + * + * @private + * @param {Array|Object} collection The collection to iterate over. + * @param {Function} predicate The function invoked per iteration. + * @returns {boolean} Returns `true` if all elements pass the predicate check, + * else `false` + */ + function baseEvery(collection, predicate) { + var result = true; + baseEach(collection, function(value, index, collection) { + result = !!predicate(value, index, collection); + return result; + }); + return result; + } + + /** + * The base implementation of methods like `_.max` and `_.min` which accepts a + * `comparator` to determine the extremum value. + * + * @private + * @param {Array} array The array to iterate over. + * @param {Function} iteratee The iteratee invoked per iteration. + * @param {Function} comparator The comparator used to compare values. + * @returns {*} Returns the extremum value. + */ + function baseExtremum(array, iteratee, comparator) { + var index = -1, + length = array.length; + + while (++index < length) { + var value = array[index], + current = iteratee(value); + + if (current != null && (computed === undefined + ? (current === current && !isSymbol(current)) + : comparator(current, computed) + )) { + var computed = current, + result = value; + } + } + return result; + } + + /** + * The base implementation of `_.fill` without an iteratee call guard. + * + * @private + * @param {Array} array The array to fill. + * @param {*} value The value to fill `array` with. + * @param {number} [start=0] The start position. + * @param {number} [end=array.length] The end position. + * @returns {Array} Returns `array`. + */ + function baseFill(array, value, start, end) { + var length = array.length; + + start = toInteger(start); + if (start < 0) { + start = -start > length ? 0 : (length + start); + } + end = (end === undefined || end > length) ? length : toInteger(end); + if (end < 0) { + end += length; + } + end = start > end ? 0 : toLength(end); + while (start < end) { + array[start++] = value; + } + return array; + } + + /** + * The base implementation of `_.filter` without support for iteratee shorthands. + * + * @private + * @param {Array|Object} collection The collection to iterate over. + * @param {Function} predicate The function invoked per iteration. + * @returns {Array} Returns the new filtered array. + */ + function baseFilter(collection, predicate) { + var result = []; + baseEach(collection, function(value, index, collection) { + if (predicate(value, index, collection)) { + result.push(value); + } + }); + return result; + } + + /** + * The base implementation of `_.flatten` with support for restricting flattening. + * + * @private + * @param {Array} array The array to flatten. + * @param {number} depth The maximum recursion depth. + * @param {boolean} [predicate=isFlattenable] The function invoked per iteration. + * @param {boolean} [isStrict] Restrict to values that pass `predicate` checks. + * @param {Array} [result=[]] The initial result value. + * @returns {Array} Returns the new flattened array. + */ + function baseFlatten(array, depth, predicate, isStrict, result) { + var index = -1, + length = array.length; + + predicate || (predicate = isFlattenable); + result || (result = []); + + while (++index < length) { + var value = array[index]; + if (depth > 0 && predicate(value)) { + if (depth > 1) { + // Recursively flatten arrays (susceptible to call stack limits). + baseFlatten(value, depth - 1, predicate, isStrict, result); + } else { + arrayPush(result, value); + } + } else if (!isStrict) { + result[result.length] = value; + } + } + return result; + } + + /** + * The base implementation of `baseForOwn` which iterates over `object` + * properties returned by `keysFunc` and invokes `iteratee` for each property. + * Iteratee functions may exit iteration early by explicitly returning `false`. + * + * @private + * @param {Object} object The object to iterate over. + * @param {Function} iteratee The function invoked per iteration. + * @param {Function} keysFunc The function to get the keys of `object`. + * @returns {Object} Returns `object`. + */ + var baseFor = createBaseFor(); + + /** + * This function is like `baseFor` except that it iterates over properties + * in the opposite order. + * + * @private + * @param {Object} object The object to iterate over. + * @param {Function} iteratee The function invoked per iteration. + * @param {Function} keysFunc The function to get the keys of `object`. + * @returns {Object} Returns `object`. + */ + var baseForRight = createBaseFor(true); + + /** + * The base implementation of `_.forOwn` without support for iteratee shorthands. + * + * @private + * @param {Object} object The object to iterate over. + * @param {Function} iteratee The function invoked per iteration. + * @returns {Object} Returns `object`. + */ + function baseForOwn(object, iteratee) { + return object && baseFor(object, iteratee, keys); + } + + /** + * The base implementation of `_.forOwnRight` without support for iteratee shorthands. + * + * @private + * @param {Object} object The object to iterate over. + * @param {Function} iteratee The function invoked per iteration. + * @returns {Object} Returns `object`. + */ + function baseForOwnRight(object, iteratee) { + return object && baseForRight(object, iteratee, keys); + } + + /** + * The base implementation of `_.functions` which creates an array of + * `object` function property names filtered from `props`. + * + * @private + * @param {Object} object The object to inspect. + * @param {Array} props The property names to filter. + * @returns {Array} Returns the function names. + */ + function baseFunctions(object, props) { + return arrayFilter(props, function(key) { + return isFunction(object[key]); + }); + } + + /** + * The base implementation of `_.get` without support for default values. + * + * @private + * @param {Object} object The object to query. + * @param {Array|string} path The path of the property to get. + * @returns {*} Returns the resolved value. + */ + function baseGet(object, path) { + path = castPath(path, object); + + var index = 0, + length = path.length; + + while (object != null && index < length) { + object = object[toKey(path[index++])]; + } + return (index && index == length) ? object : undefined; + } + + /** + * The base implementation of `getAllKeys` and `getAllKeysIn` which uses + * `keysFunc` and `symbolsFunc` to get the enumerable property names and + * symbols of `object`. + * + * @private + * @param {Object} object The object to query. + * @param {Function} keysFunc The function to get the keys of `object`. + * @param {Function} symbolsFunc The function to get the symbols of `object`. + * @returns {Array} Returns the array of property names and symbols. + */ + function baseGetAllKeys(object, keysFunc, symbolsFunc) { + var result = keysFunc(object); + return isArray(object) ? result : arrayPush(result, symbolsFunc(object)); + } + + /** + * The base implementation of `getTag` without fallbacks for buggy environments. + * + * @private + * @param {*} value The value to query. + * @returns {string} Returns the `toStringTag`. + */ + function baseGetTag(value) { + if (value == null) { + return value === undefined ? undefinedTag : nullTag; + } + return (symToStringTag && symToStringTag in Object(value)) + ? getRawTag(value) + : objectToString(value); + } + + /** + * The base implementation of `_.gt` which doesn't coerce arguments. + * + * @private + * @param {*} value The value to compare. + * @param {*} other The other value to compare. + * @returns {boolean} Returns `true` if `value` is greater than `other`, + * else `false`. + */ + function baseGt(value, other) { + return value > other; + } + + /** + * The base implementation of `_.has` without support for deep paths. + * + * @private + * @param {Object} [object] The object to query. + * @param {Array|string} key The key to check. + * @returns {boolean} Returns `true` if `key` exists, else `false`. + */ + function baseHas(object, key) { + return object != null && hasOwnProperty.call(object, key); + } + + /** + * The base implementation of `_.hasIn` without support for deep paths. + * + * @private + * @param {Object} [object] The object to query. + * @param {Array|string} key The key to check. + * @returns {boolean} Returns `true` if `key` exists, else `false`. + */ + function baseHasIn(object, key) { + return object != null && key in Object(object); + } + + /** + * The base implementation of `_.inRange` which doesn't coerce arguments. + * + * @private + * @param {number} number The number to check. + * @param {number} start The start of the range. + * @param {number} end The end of the range. + * @returns {boolean} Returns `true` if `number` is in the range, else `false`. + */ + function baseInRange(number, start, end) { + return number >= nativeMin(start, end) && number < nativeMax(start, end); + } + + /** + * The base implementation of methods like `_.intersection`, without support + * for iteratee shorthands, that accepts an array of arrays to inspect. + * + * @private + * @param {Array} arrays The arrays to inspect. + * @param {Function} [iteratee] The iteratee invoked per element. + * @param {Function} [comparator] The comparator invoked per element. + * @returns {Array} Returns the new array of shared values. + */ + function baseIntersection(arrays, iteratee, comparator) { + var includes = comparator ? arrayIncludesWith : arrayIncludes, + length = arrays[0].length, + othLength = arrays.length, + othIndex = othLength, + caches = Array(othLength), + maxLength = Infinity, + result = []; + + while (othIndex--) { + var array = arrays[othIndex]; + if (othIndex && iteratee) { + array = arrayMap(array, baseUnary(iteratee)); + } + maxLength = nativeMin(array.length, maxLength); + caches[othIndex] = !comparator && (iteratee || (length >= 120 && array.length >= 120)) + ? new SetCache(othIndex && array) + : undefined; + } + array = arrays[0]; + + var index = -1, + seen = caches[0]; + + outer: + while (++index < length && result.length < maxLength) { + var value = array[index], + computed = iteratee ? iteratee(value) : value; + + value = (comparator || value !== 0) ? value : 0; + if (!(seen + ? cacheHas(seen, computed) + : includes(result, computed, comparator) + )) { + othIndex = othLength; + while (--othIndex) { + var cache = caches[othIndex]; + if (!(cache + ? cacheHas(cache, computed) + : includes(arrays[othIndex], computed, comparator)) + ) { + continue outer; + } + } + if (seen) { + seen.push(computed); + } + result.push(value); + } + } + return result; + } + + /** + * The base implementation of `_.invert` and `_.invertBy` which inverts + * `object` with values transformed by `iteratee` and set by `setter`. + * + * @private + * @param {Object} object The object to iterate over. + * @param {Function} setter The function to set `accumulator` values. + * @param {Function} iteratee The iteratee to transform values. + * @param {Object} accumulator The initial inverted object. + * @returns {Function} Returns `accumulator`. + */ + function baseInverter(object, setter, iteratee, accumulator) { + baseForOwn(object, function(value, key, object) { + setter(accumulator, iteratee(value), key, object); + }); + return accumulator; + } + + /** + * The base implementation of `_.invoke` without support for individual + * method arguments. + * + * @private + * @param {Object} object The object to query. + * @param {Array|string} path The path of the method to invoke. + * @param {Array} args The arguments to invoke the method with. + * @returns {*} Returns the result of the invoked method. + */ + function baseInvoke(object, path, args) { + path = castPath(path, object); + object = parent(object, path); + var func = object == null ? object : object[toKey(last(path))]; + return func == null ? undefined : apply(func, object, args); + } + + /** + * The base implementation of `_.isArguments`. + * + * @private + * @param {*} value The value to check. + * @returns {boolean} Returns `true` if `value` is an `arguments` object, + */ + function baseIsArguments(value) { + return isObjectLike(value) && baseGetTag(value) == argsTag; + } + + /** + * The base implementation of `_.isArrayBuffer` without Node.js optimizations. + * + * @private + * @param {*} value The value to check. + * @returns {boolean} Returns `true` if `value` is an array buffer, else `false`. + */ + function baseIsArrayBuffer(value) { + return isObjectLike(value) && baseGetTag(value) == arrayBufferTag; + } + + /** + * The base implementation of `_.isDate` without Node.js optimizations. + * + * @private + * @param {*} value The value to check. + * @returns {boolean} Returns `true` if `value` is a date object, else `false`. + */ + function baseIsDate(value) { + return isObjectLike(value) && baseGetTag(value) == dateTag; + } + + /** + * The base implementation of `_.isEqual` which supports partial comparisons + * and tracks traversed objects. + * + * @private + * @param {*} value The value to compare. + * @param {*} other The other value to compare. + * @param {boolean} bitmask The bitmask flags. + * 1 - Unordered comparison + * 2 - Partial comparison + * @param {Function} [customizer] The function to customize comparisons. + * @param {Object} [stack] Tracks traversed `value` and `other` objects. + * @returns {boolean} Returns `true` if the values are equivalent, else `false`. + */ + function baseIsEqual(value, other, bitmask, customizer, stack) { + if (value === other) { + return true; + } + if (value == null || other == null || (!isObjectLike(value) && !isObjectLike(other))) { + return value !== value && other !== other; + } + return baseIsEqualDeep(value, other, bitmask, customizer, baseIsEqual, stack); + } + + /** + * A specialized version of `baseIsEqual` for arrays and objects which performs + * deep comparisons and tracks traversed objects enabling objects with circular + * references to be compared. + * + * @private + * @param {Object} object The object to compare. + * @param {Object} other The other object to compare. + * @param {number} bitmask The bitmask flags. See `baseIsEqual` for more details. + * @param {Function} customizer The function to customize comparisons. + * @param {Function} equalFunc The function to determine equivalents of values. + * @param {Object} [stack] Tracks traversed `object` and `other` objects. + * @returns {boolean} Returns `true` if the objects are equivalent, else `false`. + */ + function baseIsEqualDeep(object, other, bitmask, customizer, equalFunc, stack) { + var objIsArr = isArray(object), + othIsArr = isArray(other), + objTag = objIsArr ? arrayTag : getTag(object), + othTag = othIsArr ? arrayTag : getTag(other); + + objTag = objTag == argsTag ? objectTag : objTag; + othTag = othTag == argsTag ? objectTag : othTag; + + var objIsObj = objTag == objectTag, + othIsObj = othTag == objectTag, + isSameTag = objTag == othTag; + + if (isSameTag && isBuffer(object)) { + if (!isBuffer(other)) { + return false; + } + objIsArr = true; + objIsObj = false; + } + if (isSameTag && !objIsObj) { + stack || (stack = new Stack); + return (objIsArr || isTypedArray(object)) + ? equalArrays(object, other, bitmask, customizer, equalFunc, stack) + : equalByTag(object, other, objTag, bitmask, customizer, equalFunc, stack); + } + if (!(bitmask & COMPARE_PARTIAL_FLAG)) { + var objIsWrapped = objIsObj && hasOwnProperty.call(object, '__wrapped__'), + othIsWrapped = othIsObj && hasOwnProperty.call(other, '__wrapped__'); + + if (objIsWrapped || othIsWrapped) { + var objUnwrapped = objIsWrapped ? object.value() : object, + othUnwrapped = othIsWrapped ? other.value() : other; + + stack || (stack = new Stack); + return equalFunc(objUnwrapped, othUnwrapped, bitmask, customizer, stack); + } + } + if (!isSameTag) { + return false; + } + stack || (stack = new Stack); + return equalObjects(object, other, bitmask, customizer, equalFunc, stack); + } + + /** + * The base implementation of `_.isMap` without Node.js optimizations. + * + * @private + * @param {*} value The value to check. + * @returns {boolean} Returns `true` if `value` is a map, else `false`. + */ + function baseIsMap(value) { + return isObjectLike(value) && getTag(value) == mapTag; + } + + /** + * The base implementation of `_.isMatch` without support for iteratee shorthands. + * + * @private + * @param {Object} object The object to inspect. + * @param {Object} source The object of property values to match. + * @param {Array} matchData The property names, values, and compare flags to match. + * @param {Function} [customizer] The function to customize comparisons. + * @returns {boolean} Returns `true` if `object` is a match, else `false`. + */ + function baseIsMatch(object, source, matchData, customizer) { + var index = matchData.length, + length = index, + noCustomizer = !customizer; + + if (object == null) { + return !length; + } + object = Object(object); + while (index--) { + var data = matchData[index]; + if ((noCustomizer && data[2]) + ? data[1] !== object[data[0]] + : !(data[0] in object) + ) { + return false; + } + } + while (++index < length) { + data = matchData[index]; + var key = data[0], + objValue = object[key], + srcValue = data[1]; + + if (noCustomizer && data[2]) { + if (objValue === undefined && !(key in object)) { + return false; + } + } else { + var stack = new Stack; + if (customizer) { + var result = customizer(objValue, srcValue, key, object, source, stack); + } + if (!(result === undefined + ? baseIsEqual(srcValue, objValue, COMPARE_PARTIAL_FLAG | COMPARE_UNORDERED_FLAG, customizer, stack) + : result + )) { + return false; + } + } + } + return true; + } + + /** + * The base implementation of `_.isNative` without bad shim checks. + * + * @private + * @param {*} value The value to check. + * @returns {boolean} Returns `true` if `value` is a native function, + * else `false`. + */ + function baseIsNative(value) { + if (!isObject(value) || isMasked(value)) { + return false; + } + var pattern = isFunction(value) ? reIsNative : reIsHostCtor; + return pattern.test(toSource(value)); + } + + /** + * The base implementation of `_.isRegExp` without Node.js optimizations. + * + * @private + * @param {*} value The value to check. + * @returns {boolean} Returns `true` if `value` is a regexp, else `false`. + */ + function baseIsRegExp(value) { + return isObjectLike(value) && baseGetTag(value) == regexpTag; + } + + /** + * The base implementation of `_.isSet` without Node.js optimizations. + * + * @private + * @param {*} value The value to check. + * @returns {boolean} Returns `true` if `value` is a set, else `false`. + */ + function baseIsSet(value) { + return isObjectLike(value) && getTag(value) == setTag; + } + + /** + * The base implementation of `_.isTypedArray` without Node.js optimizations. + * + * @private + * @param {*} value The value to check. + * @returns {boolean} Returns `true` if `value` is a typed array, else `false`. + */ + function baseIsTypedArray(value) { + return isObjectLike(value) && + isLength(value.length) && !!typedArrayTags[baseGetTag(value)]; + } + + /** + * The base implementation of `_.iteratee`. + * + * @private + * @param {*} [value=_.identity] The value to convert to an iteratee. + * @returns {Function} Returns the iteratee. + */ + function baseIteratee(value) { + // Don't store the `typeof` result in a variable to avoid a JIT bug in Safari 9. + // See https://bugs.webkit.org/show_bug.cgi?id=156034 for more details. + if (typeof value == 'function') { + return value; + } + if (value == null) { + return identity; + } + if (typeof value == 'object') { + return isArray(value) + ? baseMatchesProperty(value[0], value[1]) + : baseMatches(value); + } + return property(value); + } + + /** + * The base implementation of `_.keys` which doesn't treat sparse arrays as dense. + * + * @private + * @param {Object} object The object to query. + * @returns {Array} Returns the array of property names. + */ + function baseKeys(object) { + if (!isPrototype(object)) { + return nativeKeys(object); + } + var result = []; + for (var key in Object(object)) { + if (hasOwnProperty.call(object, key) && key != 'constructor') { + result.push(key); + } + } + return result; + } + + /** + * The base implementation of `_.keysIn` which doesn't treat sparse arrays as dense. + * + * @private + * @param {Object} object The object to query. + * @returns {Array} Returns the array of property names. + */ + function baseKeysIn(object) { + if (!isObject(object)) { + return nativeKeysIn(object); + } + var isProto = isPrototype(object), + result = []; + + for (var key in object) { + if (!(key == 'constructor' && (isProto || !hasOwnProperty.call(object, key)))) { + result.push(key); + } + } + return result; + } + + /** + * The base implementation of `_.lt` which doesn't coerce arguments. + * + * @private + * @param {*} value The value to compare. + * @param {*} other The other value to compare. + * @returns {boolean} Returns `true` if `value` is less than `other`, + * else `false`. + */ + function baseLt(value, other) { + return value < other; + } + + /** + * The base implementation of `_.map` without support for iteratee shorthands. + * + * @private + * @param {Array|Object} collection The collection to iterate over. + * @param {Function} iteratee The function invoked per iteration. + * @returns {Array} Returns the new mapped array. + */ + function baseMap(collection, iteratee) { + var index = -1, + result = isArrayLike(collection) ? Array(collection.length) : []; + + baseEach(collection, function(value, key, collection) { + result[++index] = iteratee(value, key, collection); + }); + return result; + } + + /** + * The base implementation of `_.matches` which doesn't clone `source`. + * + * @private + * @param {Object} source The object of property values to match. + * @returns {Function} Returns the new spec function. + */ + function baseMatches(source) { + var matchData = getMatchData(source); + if (matchData.length == 1 && matchData[0][2]) { + return matchesStrictComparable(matchData[0][0], matchData[0][1]); + } + return function(object) { + return object === source || baseIsMatch(object, source, matchData); + }; + } + + /** + * The base implementation of `_.matchesProperty` which doesn't clone `srcValue`. + * + * @private + * @param {string} path The path of the property to get. + * @param {*} srcValue The value to match. + * @returns {Function} Returns the new spec function. + */ + function baseMatchesProperty(path, srcValue) { + if (isKey(path) && isStrictComparable(srcValue)) { + return matchesStrictComparable(toKey(path), srcValue); + } + return function(object) { + var objValue = get(object, path); + return (objValue === undefined && objValue === srcValue) + ? hasIn(object, path) + : baseIsEqual(srcValue, objValue, COMPARE_PARTIAL_FLAG | COMPARE_UNORDERED_FLAG); + }; + } + + /** + * The base implementation of `_.merge` without support for multiple sources. + * + * @private + * @param {Object} object The destination object. + * @param {Object} source The source object. + * @param {number} srcIndex The index of `source`. + * @param {Function} [customizer] The function to customize merged values. + * @param {Object} [stack] Tracks traversed source values and their merged + * counterparts. + */ + function baseMerge(object, source, srcIndex, customizer, stack) { + if (object === source) { + return; + } + baseFor(source, function(srcValue, key) { + stack || (stack = new Stack); + if (isObject(srcValue)) { + baseMergeDeep(object, source, key, srcIndex, baseMerge, customizer, stack); + } + else { + var newValue = customizer + ? customizer(safeGet(object, key), srcValue, (key + ''), object, source, stack) + : undefined; + + if (newValue === undefined) { + newValue = srcValue; + } + assignMergeValue(object, key, newValue); + } + }, keysIn); + } + + /** + * A specialized version of `baseMerge` for arrays and objects which performs + * deep merges and tracks traversed objects enabling objects with circular + * references to be merged. + * + * @private + * @param {Object} object The destination object. + * @param {Object} source The source object. + * @param {string} key The key of the value to merge. + * @param {number} srcIndex The index of `source`. + * @param {Function} mergeFunc The function to merge values. + * @param {Function} [customizer] The function to customize assigned values. + * @param {Object} [stack] Tracks traversed source values and their merged + * counterparts. + */ + function baseMergeDeep(object, source, key, srcIndex, mergeFunc, customizer, stack) { + var objValue = safeGet(object, key), + srcValue = safeGet(source, key), + stacked = stack.get(srcValue); + + if (stacked) { + assignMergeValue(object, key, stacked); + return; + } + var newValue = customizer + ? customizer(objValue, srcValue, (key + ''), object, source, stack) + : undefined; + + var isCommon = newValue === undefined; + + if (isCommon) { + var isArr = isArray(srcValue), + isBuff = !isArr && isBuffer(srcValue), + isTyped = !isArr && !isBuff && isTypedArray(srcValue); + + newValue = srcValue; + if (isArr || isBuff || isTyped) { + if (isArray(objValue)) { + newValue = objValue; + } + else if (isArrayLikeObject(objValue)) { + newValue = copyArray(objValue); + } + else if (isBuff) { + isCommon = false; + newValue = cloneBuffer(srcValue, true); + } + else if (isTyped) { + isCommon = false; + newValue = cloneTypedArray(srcValue, true); + } + else { + newValue = []; + } + } + else if (isPlainObject(srcValue) || isArguments(srcValue)) { + newValue = objValue; + if (isArguments(objValue)) { + newValue = toPlainObject(objValue); + } + else if (!isObject(objValue) || isFunction(objValue)) { + newValue = initCloneObject(srcValue); + } + } + else { + isCommon = false; + } + } + if (isCommon) { + // Recursively merge objects and arrays (susceptible to call stack limits). + stack.set(srcValue, newValue); + mergeFunc(newValue, srcValue, srcIndex, customizer, stack); + stack['delete'](srcValue); + } + assignMergeValue(object, key, newValue); + } + + /** + * The base implementation of `_.nth` which doesn't coerce arguments. + * + * @private + * @param {Array} array The array to query. + * @param {number} n The index of the element to return. + * @returns {*} Returns the nth element of `array`. + */ + function baseNth(array, n) { + var length = array.length; + if (!length) { + return; + } + n += n < 0 ? length : 0; + return isIndex(n, length) ? array[n] : undefined; + } + + /** + * The base implementation of `_.orderBy` without param guards. + * + * @private + * @param {Array|Object} collection The collection to iterate over. + * @param {Function[]|Object[]|string[]} iteratees The iteratees to sort by. + * @param {string[]} orders The sort orders of `iteratees`. + * @returns {Array} Returns the new sorted array. + */ + function baseOrderBy(collection, iteratees, orders) { + if (iteratees.length) { + iteratees = arrayMap(iteratees, function(iteratee) { + if (isArray(iteratee)) { + return function(value) { + return baseGet(value, iteratee.length === 1 ? iteratee[0] : iteratee); + } + } + return iteratee; + }); + } else { + iteratees = [identity]; + } + + var index = -1; + iteratees = arrayMap(iteratees, baseUnary(getIteratee())); + + var result = baseMap(collection, function(value, key, collection) { + var criteria = arrayMap(iteratees, function(iteratee) { + return iteratee(value); + }); + return { 'criteria': criteria, 'index': ++index, 'value': value }; + }); + + return baseSortBy(result, function(object, other) { + return compareMultiple(object, other, orders); + }); + } + + /** + * The base implementation of `_.pick` without support for individual + * property identifiers. + * + * @private + * @param {Object} object The source object. + * @param {string[]} paths The property paths to pick. + * @returns {Object} Returns the new object. + */ + function basePick(object, paths) { + return basePickBy(object, paths, function(value, path) { + return hasIn(object, path); + }); + } + + /** + * The base implementation of `_.pickBy` without support for iteratee shorthands. + * + * @private + * @param {Object} object The source object. + * @param {string[]} paths The property paths to pick. + * @param {Function} predicate The function invoked per property. + * @returns {Object} Returns the new object. + */ + function basePickBy(object, paths, predicate) { + var index = -1, + length = paths.length, + result = {}; + + while (++index < length) { + var path = paths[index], + value = baseGet(object, path); + + if (predicate(value, path)) { + baseSet(result, castPath(path, object), value); + } + } + return result; + } + + /** + * A specialized version of `baseProperty` which supports deep paths. + * + * @private + * @param {Array|string} path The path of the property to get. + * @returns {Function} Returns the new accessor function. + */ + function basePropertyDeep(path) { + return function(object) { + return baseGet(object, path); + }; + } + + /** + * The base implementation of `_.pullAllBy` without support for iteratee + * shorthands. + * + * @private + * @param {Array} array The array to modify. + * @param {Array} values The values to remove. + * @param {Function} [iteratee] The iteratee invoked per element. + * @param {Function} [comparator] The comparator invoked per element. + * @returns {Array} Returns `array`. + */ + function basePullAll(array, values, iteratee, comparator) { + var indexOf = comparator ? baseIndexOfWith : baseIndexOf, + index = -1, + length = values.length, + seen = array; + + if (array === values) { + values = copyArray(values); + } + if (iteratee) { + seen = arrayMap(array, baseUnary(iteratee)); + } + while (++index < length) { + var fromIndex = 0, + value = values[index], + computed = iteratee ? iteratee(value) : value; + + while ((fromIndex = indexOf(seen, computed, fromIndex, comparator)) > -1) { + if (seen !== array) { + splice.call(seen, fromIndex, 1); + } + splice.call(array, fromIndex, 1); + } + } + return array; + } + + /** + * The base implementation of `_.pullAt` without support for individual + * indexes or capturing the removed elements. + * + * @private + * @param {Array} array The array to modify. + * @param {number[]} indexes The indexes of elements to remove. + * @returns {Array} Returns `array`. + */ + function basePullAt(array, indexes) { + var length = array ? indexes.length : 0, + lastIndex = length - 1; + + while (length--) { + var index = indexes[length]; + if (length == lastIndex || index !== previous) { + var previous = index; + if (isIndex(index)) { + splice.call(array, index, 1); + } else { + baseUnset(array, index); + } + } + } + return array; + } + + /** + * The base implementation of `_.random` without support for returning + * floating-point numbers. + * + * @private + * @param {number} lower The lower bound. + * @param {number} upper The upper bound. + * @returns {number} Returns the random number. + */ + function baseRandom(lower, upper) { + return lower + nativeFloor(nativeRandom() * (upper - lower + 1)); + } + + /** + * The base implementation of `_.range` and `_.rangeRight` which doesn't + * coerce arguments. + * + * @private + * @param {number} start The start of the range. + * @param {number} end The end of the range. + * @param {number} step The value to increment or decrement by. + * @param {boolean} [fromRight] Specify iterating from right to left. + * @returns {Array} Returns the range of numbers. + */ + function baseRange(start, end, step, fromRight) { + var index = -1, + length = nativeMax(nativeCeil((end - start) / (step || 1)), 0), + result = Array(length); + + while (length--) { + result[fromRight ? length : ++index] = start; + start += step; + } + return result; + } + + /** + * The base implementation of `_.repeat` which doesn't coerce arguments. + * + * @private + * @param {string} string The string to repeat. + * @param {number} n The number of times to repeat the string. + * @returns {string} Returns the repeated string. + */ + function baseRepeat(string, n) { + var result = ''; + if (!string || n < 1 || n > MAX_SAFE_INTEGER) { + return result; + } + // Leverage the exponentiation by squaring algorithm for a faster repeat. + // See https://en.wikipedia.org/wiki/Exponentiation_by_squaring for more details. + do { + if (n % 2) { + result += string; + } + n = nativeFloor(n / 2); + if (n) { + string += string; + } + } while (n); + + return result; + } + + /** + * The base implementation of `_.rest` which doesn't validate or coerce arguments. + * + * @private + * @param {Function} func The function to apply a rest parameter to. + * @param {number} [start=func.length-1] The start position of the rest parameter. + * @returns {Function} Returns the new function. + */ + function baseRest(func, start) { + return setToString(overRest(func, start, identity), func + ''); + } + + /** + * The base implementation of `_.sample`. + * + * @private + * @param {Array|Object} collection The collection to sample. + * @returns {*} Returns the random element. + */ + function baseSample(collection) { + return arraySample(values(collection)); + } + + /** + * The base implementation of `_.sampleSize` without param guards. + * + * @private + * @param {Array|Object} collection The collection to sample. + * @param {number} n The number of elements to sample. + * @returns {Array} Returns the random elements. + */ + function baseSampleSize(collection, n) { + var array = values(collection); + return shuffleSelf(array, baseClamp(n, 0, array.length)); + } + + /** + * The base implementation of `_.set`. + * + * @private + * @param {Object} object The object to modify. + * @param {Array|string} path The path of the property to set. + * @param {*} value The value to set. + * @param {Function} [customizer] The function to customize path creation. + * @returns {Object} Returns `object`. + */ + function baseSet(object, path, value, customizer) { + if (!isObject(object)) { + return object; + } + path = castPath(path, object); + + var index = -1, + length = path.length, + lastIndex = length - 1, + nested = object; + + while (nested != null && ++index < length) { + var key = toKey(path[index]), + newValue = value; + + if (key === '__proto__' || key === 'constructor' || key === 'prototype') { + return object; + } + + if (index != lastIndex) { + var objValue = nested[key]; + newValue = customizer ? customizer(objValue, key, nested) : undefined; + if (newValue === undefined) { + newValue = isObject(objValue) + ? objValue + : (isIndex(path[index + 1]) ? [] : {}); + } + } + assignValue(nested, key, newValue); + nested = nested[key]; + } + return object; + } + + /** + * The base implementation of `setData` without support for hot loop shorting. + * + * @private + * @param {Function} func The function to associate metadata with. + * @param {*} data The metadata. + * @returns {Function} Returns `func`. + */ + var baseSetData = !metaMap ? identity : function(func, data) { + metaMap.set(func, data); + return func; + }; + + /** + * The base implementation of `setToString` without support for hot loop shorting. + * + * @private + * @param {Function} func The function to modify. + * @param {Function} string The `toString` result. + * @returns {Function} Returns `func`. + */ + var baseSetToString = !defineProperty ? identity : function(func, string) { + return defineProperty(func, 'toString', { + 'configurable': true, + 'enumerable': false, + 'value': constant(string), + 'writable': true + }); + }; + + /** + * The base implementation of `_.shuffle`. + * + * @private + * @param {Array|Object} collection The collection to shuffle. + * @returns {Array} Returns the new shuffled array. + */ + function baseShuffle(collection) { + return shuffleSelf(values(collection)); + } + + /** + * The base implementation of `_.slice` without an iteratee call guard. + * + * @private + * @param {Array} array The array to slice. + * @param {number} [start=0] The start position. + * @param {number} [end=array.length] The end position. + * @returns {Array} Returns the slice of `array`. + */ + function baseSlice(array, start, end) { + var index = -1, + length = array.length; + + if (start < 0) { + start = -start > length ? 0 : (length + start); + } + end = end > length ? length : end; + if (end < 0) { + end += length; + } + length = start > end ? 0 : ((end - start) >>> 0); + start >>>= 0; + + var result = Array(length); + while (++index < length) { + result[index] = array[index + start]; + } + return result; + } + + /** + * The base implementation of `_.some` without support for iteratee shorthands. + * + * @private + * @param {Array|Object} collection The collection to iterate over. + * @param {Function} predicate The function invoked per iteration. + * @returns {boolean} Returns `true` if any element passes the predicate check, + * else `false`. + */ + function baseSome(collection, predicate) { + var result; + + baseEach(collection, function(value, index, collection) { + result = predicate(value, index, collection); + return !result; + }); + return !!result; + } + + /** + * The base implementation of `_.sortedIndex` and `_.sortedLastIndex` which + * performs a binary search of `array` to determine the index at which `value` + * should be inserted into `array` in order to maintain its sort order. + * + * @private + * @param {Array} array The sorted array to inspect. + * @param {*} value The value to evaluate. + * @param {boolean} [retHighest] Specify returning the highest qualified index. + * @returns {number} Returns the index at which `value` should be inserted + * into `array`. + */ + function baseSortedIndex(array, value, retHighest) { + var low = 0, + high = array == null ? low : array.length; + + if (typeof value == 'number' && value === value && high <= HALF_MAX_ARRAY_LENGTH) { + while (low < high) { + var mid = (low + high) >>> 1, + computed = array[mid]; + + if (computed !== null && !isSymbol(computed) && + (retHighest ? (computed <= value) : (computed < value))) { + low = mid + 1; + } else { + high = mid; + } + } + return high; + } + return baseSortedIndexBy(array, value, identity, retHighest); + } + + /** + * The base implementation of `_.sortedIndexBy` and `_.sortedLastIndexBy` + * which invokes `iteratee` for `value` and each element of `array` to compute + * their sort ranking. The iteratee is invoked with one argument; (value). + * + * @private + * @param {Array} array The sorted array to inspect. + * @param {*} value The value to evaluate. + * @param {Function} iteratee The iteratee invoked per element. + * @param {boolean} [retHighest] Specify returning the highest qualified index. + * @returns {number} Returns the index at which `value` should be inserted + * into `array`. + */ + function baseSortedIndexBy(array, value, iteratee, retHighest) { + var low = 0, + high = array == null ? 0 : array.length; + if (high === 0) { + return 0; + } + + value = iteratee(value); + var valIsNaN = value !== value, + valIsNull = value === null, + valIsSymbol = isSymbol(value), + valIsUndefined = value === undefined; + + while (low < high) { + var mid = nativeFloor((low + high) / 2), + computed = iteratee(array[mid]), + othIsDefined = computed !== undefined, + othIsNull = computed === null, + othIsReflexive = computed === computed, + othIsSymbol = isSymbol(computed); + + if (valIsNaN) { + var setLow = retHighest || othIsReflexive; + } else if (valIsUndefined) { + setLow = othIsReflexive && (retHighest || othIsDefined); + } else if (valIsNull) { + setLow = othIsReflexive && othIsDefined && (retHighest || !othIsNull); + } else if (valIsSymbol) { + setLow = othIsReflexive && othIsDefined && !othIsNull && (retHighest || !othIsSymbol); + } else if (othIsNull || othIsSymbol) { + setLow = false; + } else { + setLow = retHighest ? (computed <= value) : (computed < value); + } + if (setLow) { + low = mid + 1; + } else { + high = mid; + } + } + return nativeMin(high, MAX_ARRAY_INDEX); + } + + /** + * The base implementation of `_.sortedUniq` and `_.sortedUniqBy` without + * support for iteratee shorthands. + * + * @private + * @param {Array} array The array to inspect. + * @param {Function} [iteratee] The iteratee invoked per element. + * @returns {Array} Returns the new duplicate free array. + */ + function baseSortedUniq(array, iteratee) { + var index = -1, + length = array.length, + resIndex = 0, + result = []; + + while (++index < length) { + var value = array[index], + computed = iteratee ? iteratee(value) : value; + + if (!index || !eq(computed, seen)) { + var seen = computed; + result[resIndex++] = value === 0 ? 0 : value; + } + } + return result; + } + + /** + * The base implementation of `_.toNumber` which doesn't ensure correct + * conversions of binary, hexadecimal, or octal string values. + * + * @private + * @param {*} value The value to process. + * @returns {number} Returns the number. + */ + function baseToNumber(value) { + if (typeof value == 'number') { + return value; + } + if (isSymbol(value)) { + return NAN; + } + return +value; + } + + /** + * The base implementation of `_.toString` which doesn't convert nullish + * values to empty strings. + * + * @private + * @param {*} value The value to process. + * @returns {string} Returns the string. + */ + function baseToString(value) { + // Exit early for strings to avoid a performance hit in some environments. + if (typeof value == 'string') { + return value; + } + if (isArray(value)) { + // Recursively convert values (susceptible to call stack limits). + return arrayMap(value, baseToString) + ''; + } + if (isSymbol(value)) { + return symbolToString ? symbolToString.call(value) : ''; + } + var result = (value + ''); + return (result == '0' && (1 / value) == -INFINITY) ? '-0' : result; + } + + /** + * The base implementation of `_.uniqBy` without support for iteratee shorthands. + * + * @private + * @param {Array} array The array to inspect. + * @param {Function} [iteratee] The iteratee invoked per element. + * @param {Function} [comparator] The comparator invoked per element. + * @returns {Array} Returns the new duplicate free array. + */ + function baseUniq(array, iteratee, comparator) { + var index = -1, + includes = arrayIncludes, + length = array.length, + isCommon = true, + result = [], + seen = result; + + if (comparator) { + isCommon = false; + includes = arrayIncludesWith; + } + else if (length >= LARGE_ARRAY_SIZE) { + var set = iteratee ? null : createSet(array); + if (set) { + return setToArray(set); + } + isCommon = false; + includes = cacheHas; + seen = new SetCache; + } + else { + seen = iteratee ? [] : result; + } + outer: + while (++index < length) { + var value = array[index], + computed = iteratee ? iteratee(value) : value; + + value = (comparator || value !== 0) ? value : 0; + if (isCommon && computed === computed) { + var seenIndex = seen.length; + while (seenIndex--) { + if (seen[seenIndex] === computed) { + continue outer; + } + } + if (iteratee) { + seen.push(computed); + } + result.push(value); + } + else if (!includes(seen, computed, comparator)) { + if (seen !== result) { + seen.push(computed); + } + result.push(value); + } + } + return result; + } + + /** + * The base implementation of `_.unset`. + * + * @private + * @param {Object} object The object to modify. + * @param {Array|string} path The property path to unset. + * @returns {boolean} Returns `true` if the property is deleted, else `false`. + */ + function baseUnset(object, path) { + path = castPath(path, object); + object = parent(object, path); + return object == null || delete object[toKey(last(path))]; + } + + /** + * The base implementation of `_.update`. + * + * @private + * @param {Object} object The object to modify. + * @param {Array|string} path The path of the property to update. + * @param {Function} updater The function to produce the updated value. + * @param {Function} [customizer] The function to customize path creation. + * @returns {Object} Returns `object`. + */ + function baseUpdate(object, path, updater, customizer) { + return baseSet(object, path, updater(baseGet(object, path)), customizer); + } + + /** + * The base implementation of methods like `_.dropWhile` and `_.takeWhile` + * without support for iteratee shorthands. + * + * @private + * @param {Array} array The array to query. + * @param {Function} predicate The function invoked per iteration. + * @param {boolean} [isDrop] Specify dropping elements instead of taking them. + * @param {boolean} [fromRight] Specify iterating from right to left. + * @returns {Array} Returns the slice of `array`. + */ + function baseWhile(array, predicate, isDrop, fromRight) { + var length = array.length, + index = fromRight ? length : -1; + + while ((fromRight ? index-- : ++index < length) && + predicate(array[index], index, array)) {} + + return isDrop + ? baseSlice(array, (fromRight ? 0 : index), (fromRight ? index + 1 : length)) + : baseSlice(array, (fromRight ? index + 1 : 0), (fromRight ? length : index)); + } + + /** + * The base implementation of `wrapperValue` which returns the result of + * performing a sequence of actions on the unwrapped `value`, where each + * successive action is supplied the return value of the previous. + * + * @private + * @param {*} value The unwrapped value. + * @param {Array} actions Actions to perform to resolve the unwrapped value. + * @returns {*} Returns the resolved value. + */ + function baseWrapperValue(value, actions) { + var result = value; + if (result instanceof LazyWrapper) { + result = result.value(); + } + return arrayReduce(actions, function(result, action) { + return action.func.apply(action.thisArg, arrayPush([result], action.args)); + }, result); + } + + /** + * The base implementation of methods like `_.xor`, without support for + * iteratee shorthands, that accepts an array of arrays to inspect. + * + * @private + * @param {Array} arrays The arrays to inspect. + * @param {Function} [iteratee] The iteratee invoked per element. + * @param {Function} [comparator] The comparator invoked per element. + * @returns {Array} Returns the new array of values. + */ + function baseXor(arrays, iteratee, comparator) { + var length = arrays.length; + if (length < 2) { + return length ? baseUniq(arrays[0]) : []; + } + var index = -1, + result = Array(length); + + while (++index < length) { + var array = arrays[index], + othIndex = -1; + + while (++othIndex < length) { + if (othIndex != index) { + result[index] = baseDifference(result[index] || array, arrays[othIndex], iteratee, comparator); + } + } + } + return baseUniq(baseFlatten(result, 1), iteratee, comparator); + } + + /** + * This base implementation of `_.zipObject` which assigns values using `assignFunc`. + * + * @private + * @param {Array} props The property identifiers. + * @param {Array} values The property values. + * @param {Function} assignFunc The function to assign values. + * @returns {Object} Returns the new object. + */ + function baseZipObject(props, values, assignFunc) { + var index = -1, + length = props.length, + valsLength = values.length, + result = {}; + + while (++index < length) { + var value = index < valsLength ? values[index] : undefined; + assignFunc(result, props[index], value); + } + return result; + } + + /** + * Casts `value` to an empty array if it's not an array like object. + * + * @private + * @param {*} value The value to inspect. + * @returns {Array|Object} Returns the cast array-like object. + */ + function castArrayLikeObject(value) { + return isArrayLikeObject(value) ? value : []; + } + + /** + * Casts `value` to `identity` if it's not a function. + * + * @private + * @param {*} value The value to inspect. + * @returns {Function} Returns cast function. + */ + function castFunction(value) { + return typeof value == 'function' ? value : identity; + } + + /** + * Casts `value` to a path array if it's not one. + * + * @private + * @param {*} value The value to inspect. + * @param {Object} [object] The object to query keys on. + * @returns {Array} Returns the cast property path array. + */ + function castPath(value, object) { + if (isArray(value)) { + return value; + } + return isKey(value, object) ? [value] : stringToPath(toString(value)); + } + + /** + * A `baseRest` alias which can be replaced with `identity` by module + * replacement plugins. + * + * @private + * @type {Function} + * @param {Function} func The function to apply a rest parameter to. + * @returns {Function} Returns the new function. + */ + var castRest = baseRest; + + /** + * Casts `array` to a slice if it's needed. + * + * @private + * @param {Array} array The array to inspect. + * @param {number} start The start position. + * @param {number} [end=array.length] The end position. + * @returns {Array} Returns the cast slice. + */ + function castSlice(array, start, end) { + var length = array.length; + end = end === undefined ? length : end; + return (!start && end >= length) ? array : baseSlice(array, start, end); + } + + /** + * A simple wrapper around the global [`clearTimeout`](https://mdn.io/clearTimeout). + * + * @private + * @param {number|Object} id The timer id or timeout object of the timer to clear. + */ + var clearTimeout = ctxClearTimeout || function(id) { + return root.clearTimeout(id); + }; + + /** + * Creates a clone of `buffer`. + * + * @private + * @param {Buffer} buffer The buffer to clone. + * @param {boolean} [isDeep] Specify a deep clone. + * @returns {Buffer} Returns the cloned buffer. + */ + function cloneBuffer(buffer, isDeep) { + if (isDeep) { + return buffer.slice(); + } + var length = buffer.length, + result = allocUnsafe ? allocUnsafe(length) : new buffer.constructor(length); + + buffer.copy(result); + return result; + } + + /** + * Creates a clone of `arrayBuffer`. + * + * @private + * @param {ArrayBuffer} arrayBuffer The array buffer to clone. + * @returns {ArrayBuffer} Returns the cloned array buffer. + */ + function cloneArrayBuffer(arrayBuffer) { + var result = new arrayBuffer.constructor(arrayBuffer.byteLength); + new Uint8Array(result).set(new Uint8Array(arrayBuffer)); + return result; + } + + /** + * Creates a clone of `dataView`. + * + * @private + * @param {Object} dataView The data view to clone. + * @param {boolean} [isDeep] Specify a deep clone. + * @returns {Object} Returns the cloned data view. + */ + function cloneDataView(dataView, isDeep) { + var buffer = isDeep ? cloneArrayBuffer(dataView.buffer) : dataView.buffer; + return new dataView.constructor(buffer, dataView.byteOffset, dataView.byteLength); + } + + /** + * Creates a clone of `regexp`. + * + * @private + * @param {Object} regexp The regexp to clone. + * @returns {Object} Returns the cloned regexp. + */ + function cloneRegExp(regexp) { + var result = new regexp.constructor(regexp.source, reFlags.exec(regexp)); + result.lastIndex = regexp.lastIndex; + return result; + } + + /** + * Creates a clone of the `symbol` object. + * + * @private + * @param {Object} symbol The symbol object to clone. + * @returns {Object} Returns the cloned symbol object. + */ + function cloneSymbol(symbol) { + return symbolValueOf ? Object(symbolValueOf.call(symbol)) : {}; + } + + /** + * Creates a clone of `typedArray`. + * + * @private + * @param {Object} typedArray The typed array to clone. + * @param {boolean} [isDeep] Specify a deep clone. + * @returns {Object} Returns the cloned typed array. + */ + function cloneTypedArray(typedArray, isDeep) { + var buffer = isDeep ? cloneArrayBuffer(typedArray.buffer) : typedArray.buffer; + return new typedArray.constructor(buffer, typedArray.byteOffset, typedArray.length); + } + + /** + * Compares values to sort them in ascending order. + * + * @private + * @param {*} value The value to compare. + * @param {*} other The other value to compare. + * @returns {number} Returns the sort order indicator for `value`. + */ + function compareAscending(value, other) { + if (value !== other) { + var valIsDefined = value !== undefined, + valIsNull = value === null, + valIsReflexive = value === value, + valIsSymbol = isSymbol(value); + + var othIsDefined = other !== undefined, + othIsNull = other === null, + othIsReflexive = other === other, + othIsSymbol = isSymbol(other); + + if ((!othIsNull && !othIsSymbol && !valIsSymbol && value > other) || + (valIsSymbol && othIsDefined && othIsReflexive && !othIsNull && !othIsSymbol) || + (valIsNull && othIsDefined && othIsReflexive) || + (!valIsDefined && othIsReflexive) || + !valIsReflexive) { + return 1; + } + if ((!valIsNull && !valIsSymbol && !othIsSymbol && value < other) || + (othIsSymbol && valIsDefined && valIsReflexive && !valIsNull && !valIsSymbol) || + (othIsNull && valIsDefined && valIsReflexive) || + (!othIsDefined && valIsReflexive) || + !othIsReflexive) { + return -1; + } + } + return 0; + } + + /** + * Used by `_.orderBy` to compare multiple properties of a value to another + * and stable sort them. + * + * If `orders` is unspecified, all values are sorted in ascending order. Otherwise, + * specify an order of "desc" for descending or "asc" for ascending sort order + * of corresponding values. + * + * @private + * @param {Object} object The object to compare. + * @param {Object} other The other object to compare. + * @param {boolean[]|string[]} orders The order to sort by for each property. + * @returns {number} Returns the sort order indicator for `object`. + */ + function compareMultiple(object, other, orders) { + var index = -1, + objCriteria = object.criteria, + othCriteria = other.criteria, + length = objCriteria.length, + ordersLength = orders.length; + + while (++index < length) { + var result = compareAscending(objCriteria[index], othCriteria[index]); + if (result) { + if (index >= ordersLength) { + return result; + } + var order = orders[index]; + return result * (order == 'desc' ? -1 : 1); + } + } + // Fixes an `Array#sort` bug in the JS engine embedded in Adobe applications + // that causes it, under certain circumstances, to provide the same value for + // `object` and `other`. See https://github.com/jashkenas/underscore/pull/1247 + // for more details. + // + // This also ensures a stable sort in V8 and other engines. + // See https://bugs.chromium.org/p/v8/issues/detail?id=90 for more details. + return object.index - other.index; + } + + /** + * Creates an array that is the composition of partially applied arguments, + * placeholders, and provided arguments into a single array of arguments. + * + * @private + * @param {Array} args The provided arguments. + * @param {Array} partials The arguments to prepend to those provided. + * @param {Array} holders The `partials` placeholder indexes. + * @params {boolean} [isCurried] Specify composing for a curried function. + * @returns {Array} Returns the new array of composed arguments. + */ + function composeArgs(args, partials, holders, isCurried) { + var argsIndex = -1, + argsLength = args.length, + holdersLength = holders.length, + leftIndex = -1, + leftLength = partials.length, + rangeLength = nativeMax(argsLength - holdersLength, 0), + result = Array(leftLength + rangeLength), + isUncurried = !isCurried; + + while (++leftIndex < leftLength) { + result[leftIndex] = partials[leftIndex]; + } + while (++argsIndex < holdersLength) { + if (isUncurried || argsIndex < argsLength) { + result[holders[argsIndex]] = args[argsIndex]; + } + } + while (rangeLength--) { + result[leftIndex++] = args[argsIndex++]; + } + return result; + } + + /** + * This function is like `composeArgs` except that the arguments composition + * is tailored for `_.partialRight`. + * + * @private + * @param {Array} args The provided arguments. + * @param {Array} partials The arguments to append to those provided. + * @param {Array} holders The `partials` placeholder indexes. + * @params {boolean} [isCurried] Specify composing for a curried function. + * @returns {Array} Returns the new array of composed arguments. + */ + function composeArgsRight(args, partials, holders, isCurried) { + var argsIndex = -1, + argsLength = args.length, + holdersIndex = -1, + holdersLength = holders.length, + rightIndex = -1, + rightLength = partials.length, + rangeLength = nativeMax(argsLength - holdersLength, 0), + result = Array(rangeLength + rightLength), + isUncurried = !isCurried; + + while (++argsIndex < rangeLength) { + result[argsIndex] = args[argsIndex]; + } + var offset = argsIndex; + while (++rightIndex < rightLength) { + result[offset + rightIndex] = partials[rightIndex]; + } + while (++holdersIndex < holdersLength) { + if (isUncurried || argsIndex < argsLength) { + result[offset + holders[holdersIndex]] = args[argsIndex++]; + } + } + return result; + } + + /** + * Copies the values of `source` to `array`. + * + * @private + * @param {Array} source The array to copy values from. + * @param {Array} [array=[]] The array to copy values to. + * @returns {Array} Returns `array`. + */ + function copyArray(source, array) { + var index = -1, + length = source.length; + + array || (array = Array(length)); + while (++index < length) { + array[index] = source[index]; + } + return array; + } + + /** + * Copies properties of `source` to `object`. + * + * @private + * @param {Object} source The object to copy properties from. + * @param {Array} props The property identifiers to copy. + * @param {Object} [object={}] The object to copy properties to. + * @param {Function} [customizer] The function to customize copied values. + * @returns {Object} Returns `object`. + */ + function copyObject(source, props, object, customizer) { + var isNew = !object; + object || (object = {}); + + var index = -1, + length = props.length; + + while (++index < length) { + var key = props[index]; + + var newValue = customizer + ? customizer(object[key], source[key], key, object, source) + : undefined; + + if (newValue === undefined) { + newValue = source[key]; + } + if (isNew) { + baseAssignValue(object, key, newValue); + } else { + assignValue(object, key, newValue); + } + } + return object; + } + + /** + * Copies own symbols of `source` to `object`. + * + * @private + * @param {Object} source The object to copy symbols from. + * @param {Object} [object={}] The object to copy symbols to. + * @returns {Object} Returns `object`. + */ + function copySymbols(source, object) { + return copyObject(source, getSymbols(source), object); + } + + /** + * Copies own and inherited symbols of `source` to `object`. + * + * @private + * @param {Object} source The object to copy symbols from. + * @param {Object} [object={}] The object to copy symbols to. + * @returns {Object} Returns `object`. + */ + function copySymbolsIn(source, object) { + return copyObject(source, getSymbolsIn(source), object); + } + + /** + * Creates a function like `_.groupBy`. + * + * @private + * @param {Function} setter The function to set accumulator values. + * @param {Function} [initializer] The accumulator object initializer. + * @returns {Function} Returns the new aggregator function. + */ + function createAggregator(setter, initializer) { + return function(collection, iteratee) { + var func = isArray(collection) ? arrayAggregator : baseAggregator, + accumulator = initializer ? initializer() : {}; + + return func(collection, setter, getIteratee(iteratee, 2), accumulator); + }; + } + + /** + * Creates a function like `_.assign`. + * + * @private + * @param {Function} assigner The function to assign values. + * @returns {Function} Returns the new assigner function. + */ + function createAssigner(assigner) { + return baseRest(function(object, sources) { + var index = -1, + length = sources.length, + customizer = length > 1 ? sources[length - 1] : undefined, + guard = length > 2 ? sources[2] : undefined; + + customizer = (assigner.length > 3 && typeof customizer == 'function') + ? (length--, customizer) + : undefined; + + if (guard && isIterateeCall(sources[0], sources[1], guard)) { + customizer = length < 3 ? undefined : customizer; + length = 1; + } + object = Object(object); + while (++index < length) { + var source = sources[index]; + if (source) { + assigner(object, source, index, customizer); + } + } + return object; + }); + } + + /** + * Creates a `baseEach` or `baseEachRight` function. + * + * @private + * @param {Function} eachFunc The function to iterate over a collection. + * @param {boolean} [fromRight] Specify iterating from right to left. + * @returns {Function} Returns the new base function. + */ + function createBaseEach(eachFunc, fromRight) { + return function(collection, iteratee) { + if (collection == null) { + return collection; + } + if (!isArrayLike(collection)) { + return eachFunc(collection, iteratee); + } + var length = collection.length, + index = fromRight ? length : -1, + iterable = Object(collection); + + while ((fromRight ? index-- : ++index < length)) { + if (iteratee(iterable[index], index, iterable) === false) { + break; + } + } + return collection; + }; + } + + /** + * Creates a base function for methods like `_.forIn` and `_.forOwn`. + * + * @private + * @param {boolean} [fromRight] Specify iterating from right to left. + * @returns {Function} Returns the new base function. + */ + function createBaseFor(fromRight) { + return function(object, iteratee, keysFunc) { + var index = -1, + iterable = Object(object), + props = keysFunc(object), + length = props.length; + + while (length--) { + var key = props[fromRight ? length : ++index]; + if (iteratee(iterable[key], key, iterable) === false) { + break; + } + } + return object; + }; + } + + /** + * Creates a function that wraps `func` to invoke it with the optional `this` + * binding of `thisArg`. + * + * @private + * @param {Function} func The function to wrap. + * @param {number} bitmask The bitmask flags. See `createWrap` for more details. + * @param {*} [thisArg] The `this` binding of `func`. + * @returns {Function} Returns the new wrapped function. + */ + function createBind(func, bitmask, thisArg) { + var isBind = bitmask & WRAP_BIND_FLAG, + Ctor = createCtor(func); + + function wrapper() { + var fn = (this && this !== root && this instanceof wrapper) ? Ctor : func; + return fn.apply(isBind ? thisArg : this, arguments); + } + return wrapper; + } + + /** + * Creates a function like `_.lowerFirst`. + * + * @private + * @param {string} methodName The name of the `String` case method to use. + * @returns {Function} Returns the new case function. + */ + function createCaseFirst(methodName) { + return function(string) { + string = toString(string); + + var strSymbols = hasUnicode(string) + ? stringToArray(string) + : undefined; + + var chr = strSymbols + ? strSymbols[0] + : string.charAt(0); + + var trailing = strSymbols + ? castSlice(strSymbols, 1).join('') + : string.slice(1); + + return chr[methodName]() + trailing; + }; + } + + /** + * Creates a function like `_.camelCase`. + * + * @private + * @param {Function} callback The function to combine each word. + * @returns {Function} Returns the new compounder function. + */ + function createCompounder(callback) { + return function(string) { + return arrayReduce(words(deburr(string).replace(reApos, '')), callback, ''); + }; + } + + /** + * Creates a function that produces an instance of `Ctor` regardless of + * whether it was invoked as part of a `new` expression or by `call` or `apply`. + * + * @private + * @param {Function} Ctor The constructor to wrap. + * @returns {Function} Returns the new wrapped function. + */ + function createCtor(Ctor) { + return function() { + // Use a `switch` statement to work with class constructors. See + // http://ecma-international.org/ecma-262/7.0/#sec-ecmascript-function-objects-call-thisargument-argumentslist + // for more details. + var args = arguments; + switch (args.length) { + case 0: return new Ctor; + case 1: return new Ctor(args[0]); + case 2: return new Ctor(args[0], args[1]); + case 3: return new Ctor(args[0], args[1], args[2]); + case 4: return new Ctor(args[0], args[1], args[2], args[3]); + case 5: return new Ctor(args[0], args[1], args[2], args[3], args[4]); + case 6: return new Ctor(args[0], args[1], args[2], args[3], args[4], args[5]); + case 7: return new Ctor(args[0], args[1], args[2], args[3], args[4], args[5], args[6]); + } + var thisBinding = baseCreate(Ctor.prototype), + result = Ctor.apply(thisBinding, args); + + // Mimic the constructor's `return` behavior. + // See https://es5.github.io/#x13.2.2 for more details. + return isObject(result) ? result : thisBinding; + }; + } + + /** + * Creates a function that wraps `func` to enable currying. + * + * @private + * @param {Function} func The function to wrap. + * @param {number} bitmask The bitmask flags. See `createWrap` for more details. + * @param {number} arity The arity of `func`. + * @returns {Function} Returns the new wrapped function. + */ + function createCurry(func, bitmask, arity) { + var Ctor = createCtor(func); + + function wrapper() { + var length = arguments.length, + args = Array(length), + index = length, + placeholder = getHolder(wrapper); + + while (index--) { + args[index] = arguments[index]; + } + var holders = (length < 3 && args[0] !== placeholder && args[length - 1] !== placeholder) + ? [] + : replaceHolders(args, placeholder); + + length -= holders.length; + if (length < arity) { + return createRecurry( + func, bitmask, createHybrid, wrapper.placeholder, undefined, + args, holders, undefined, undefined, arity - length); + } + var fn = (this && this !== root && this instanceof wrapper) ? Ctor : func; + return apply(fn, this, args); + } + return wrapper; + } + + /** + * Creates a `_.find` or `_.findLast` function. + * + * @private + * @param {Function} findIndexFunc The function to find the collection index. + * @returns {Function} Returns the new find function. + */ + function createFind(findIndexFunc) { + return function(collection, predicate, fromIndex) { + var iterable = Object(collection); + if (!isArrayLike(collection)) { + var iteratee = getIteratee(predicate, 3); + collection = keys(collection); + predicate = function(key) { return iteratee(iterable[key], key, iterable); }; + } + var index = findIndexFunc(collection, predicate, fromIndex); + return index > -1 ? iterable[iteratee ? collection[index] : index] : undefined; + }; + } + + /** + * Creates a `_.flow` or `_.flowRight` function. + * + * @private + * @param {boolean} [fromRight] Specify iterating from right to left. + * @returns {Function} Returns the new flow function. + */ + function createFlow(fromRight) { + return flatRest(function(funcs) { + var length = funcs.length, + index = length, + prereq = LodashWrapper.prototype.thru; + + if (fromRight) { + funcs.reverse(); + } + while (index--) { + var func = funcs[index]; + if (typeof func != 'function') { + throw new TypeError(FUNC_ERROR_TEXT); + } + if (prereq && !wrapper && getFuncName(func) == 'wrapper') { + var wrapper = new LodashWrapper([], true); + } + } + index = wrapper ? index : length; + while (++index < length) { + func = funcs[index]; + + var funcName = getFuncName(func), + data = funcName == 'wrapper' ? getData(func) : undefined; + + if (data && isLaziable(data[0]) && + data[1] == (WRAP_ARY_FLAG | WRAP_CURRY_FLAG | WRAP_PARTIAL_FLAG | WRAP_REARG_FLAG) && + !data[4].length && data[9] == 1 + ) { + wrapper = wrapper[getFuncName(data[0])].apply(wrapper, data[3]); + } else { + wrapper = (func.length == 1 && isLaziable(func)) + ? wrapper[funcName]() + : wrapper.thru(func); + } + } + return function() { + var args = arguments, + value = args[0]; + + if (wrapper && args.length == 1 && isArray(value)) { + return wrapper.plant(value).value(); + } + var index = 0, + result = length ? funcs[index].apply(this, args) : value; + + while (++index < length) { + result = funcs[index].call(this, result); + } + return result; + }; + }); + } + + /** + * Creates a function that wraps `func` to invoke it with optional `this` + * binding of `thisArg`, partial application, and currying. + * + * @private + * @param {Function|string} func The function or method name to wrap. + * @param {number} bitmask The bitmask flags. See `createWrap` for more details. + * @param {*} [thisArg] The `this` binding of `func`. + * @param {Array} [partials] The arguments to prepend to those provided to + * the new function. + * @param {Array} [holders] The `partials` placeholder indexes. + * @param {Array} [partialsRight] The arguments to append to those provided + * to the new function. + * @param {Array} [holdersRight] The `partialsRight` placeholder indexes. + * @param {Array} [argPos] The argument positions of the new function. + * @param {number} [ary] The arity cap of `func`. + * @param {number} [arity] The arity of `func`. + * @returns {Function} Returns the new wrapped function. + */ + function createHybrid(func, bitmask, thisArg, partials, holders, partialsRight, holdersRight, argPos, ary, arity) { + var isAry = bitmask & WRAP_ARY_FLAG, + isBind = bitmask & WRAP_BIND_FLAG, + isBindKey = bitmask & WRAP_BIND_KEY_FLAG, + isCurried = bitmask & (WRAP_CURRY_FLAG | WRAP_CURRY_RIGHT_FLAG), + isFlip = bitmask & WRAP_FLIP_FLAG, + Ctor = isBindKey ? undefined : createCtor(func); + + function wrapper() { + var length = arguments.length, + args = Array(length), + index = length; + + while (index--) { + args[index] = arguments[index]; + } + if (isCurried) { + var placeholder = getHolder(wrapper), + holdersCount = countHolders(args, placeholder); + } + if (partials) { + args = composeArgs(args, partials, holders, isCurried); + } + if (partialsRight) { + args = composeArgsRight(args, partialsRight, holdersRight, isCurried); + } + length -= holdersCount; + if (isCurried && length < arity) { + var newHolders = replaceHolders(args, placeholder); + return createRecurry( + func, bitmask, createHybrid, wrapper.placeholder, thisArg, + args, newHolders, argPos, ary, arity - length + ); + } + var thisBinding = isBind ? thisArg : this, + fn = isBindKey ? thisBinding[func] : func; + + length = args.length; + if (argPos) { + args = reorder(args, argPos); + } else if (isFlip && length > 1) { + args.reverse(); + } + if (isAry && ary < length) { + args.length = ary; + } + if (this && this !== root && this instanceof wrapper) { + fn = Ctor || createCtor(fn); + } + return fn.apply(thisBinding, args); + } + return wrapper; + } + + /** + * Creates a function like `_.invertBy`. + * + * @private + * @param {Function} setter The function to set accumulator values. + * @param {Function} toIteratee The function to resolve iteratees. + * @returns {Function} Returns the new inverter function. + */ + function createInverter(setter, toIteratee) { + return function(object, iteratee) { + return baseInverter(object, setter, toIteratee(iteratee), {}); + }; + } + + /** + * Creates a function that performs a mathematical operation on two values. + * + * @private + * @param {Function} operator The function to perform the operation. + * @param {number} [defaultValue] The value used for `undefined` arguments. + * @returns {Function} Returns the new mathematical operation function. + */ + function createMathOperation(operator, defaultValue) { + return function(value, other) { + var result; + if (value === undefined && other === undefined) { + return defaultValue; + } + if (value !== undefined) { + result = value; + } + if (other !== undefined) { + if (result === undefined) { + return other; + } + if (typeof value == 'string' || typeof other == 'string') { + value = baseToString(value); + other = baseToString(other); + } else { + value = baseToNumber(value); + other = baseToNumber(other); + } + result = operator(value, other); + } + return result; + }; + } + + /** + * Creates a function like `_.over`. + * + * @private + * @param {Function} arrayFunc The function to iterate over iteratees. + * @returns {Function} Returns the new over function. + */ + function createOver(arrayFunc) { + return flatRest(function(iteratees) { + iteratees = arrayMap(iteratees, baseUnary(getIteratee())); + return baseRest(function(args) { + var thisArg = this; + return arrayFunc(iteratees, function(iteratee) { + return apply(iteratee, thisArg, args); + }); + }); + }); + } + + /** + * Creates the padding for `string` based on `length`. The `chars` string + * is truncated if the number of characters exceeds `length`. + * + * @private + * @param {number} length The padding length. + * @param {string} [chars=' '] The string used as padding. + * @returns {string} Returns the padding for `string`. + */ + function createPadding(length, chars) { + chars = chars === undefined ? ' ' : baseToString(chars); + + var charsLength = chars.length; + if (charsLength < 2) { + return charsLength ? baseRepeat(chars, length) : chars; + } + var result = baseRepeat(chars, nativeCeil(length / stringSize(chars))); + return hasUnicode(chars) + ? castSlice(stringToArray(result), 0, length).join('') + : result.slice(0, length); + } + + /** + * Creates a function that wraps `func` to invoke it with the `this` binding + * of `thisArg` and `partials` prepended to the arguments it receives. + * + * @private + * @param {Function} func The function to wrap. + * @param {number} bitmask The bitmask flags. See `createWrap` for more details. + * @param {*} thisArg The `this` binding of `func`. + * @param {Array} partials The arguments to prepend to those provided to + * the new function. + * @returns {Function} Returns the new wrapped function. + */ + function createPartial(func, bitmask, thisArg, partials) { + var isBind = bitmask & WRAP_BIND_FLAG, + Ctor = createCtor(func); + + function wrapper() { + var argsIndex = -1, + argsLength = arguments.length, + leftIndex = -1, + leftLength = partials.length, + args = Array(leftLength + argsLength), + fn = (this && this !== root && this instanceof wrapper) ? Ctor : func; + + while (++leftIndex < leftLength) { + args[leftIndex] = partials[leftIndex]; + } + while (argsLength--) { + args[leftIndex++] = arguments[++argsIndex]; + } + return apply(fn, isBind ? thisArg : this, args); + } + return wrapper; + } + + /** + * Creates a `_.range` or `_.rangeRight` function. + * + * @private + * @param {boolean} [fromRight] Specify iterating from right to left. + * @returns {Function} Returns the new range function. + */ + function createRange(fromRight) { + return function(start, end, step) { + if (step && typeof step != 'number' && isIterateeCall(start, end, step)) { + end = step = undefined; + } + // Ensure the sign of `-0` is preserved. + start = toFinite(start); + if (end === undefined) { + end = start; + start = 0; + } else { + end = toFinite(end); + } + step = step === undefined ? (start < end ? 1 : -1) : toFinite(step); + return baseRange(start, end, step, fromRight); + }; + } + + /** + * Creates a function that performs a relational operation on two values. + * + * @private + * @param {Function} operator The function to perform the operation. + * @returns {Function} Returns the new relational operation function. + */ + function createRelationalOperation(operator) { + return function(value, other) { + if (!(typeof value == 'string' && typeof other == 'string')) { + value = toNumber(value); + other = toNumber(other); + } + return operator(value, other); + }; + } + + /** + * Creates a function that wraps `func` to continue currying. + * + * @private + * @param {Function} func The function to wrap. + * @param {number} bitmask The bitmask flags. See `createWrap` for more details. + * @param {Function} wrapFunc The function to create the `func` wrapper. + * @param {*} placeholder The placeholder value. + * @param {*} [thisArg] The `this` binding of `func`. + * @param {Array} [partials] The arguments to prepend to those provided to + * the new function. + * @param {Array} [holders] The `partials` placeholder indexes. + * @param {Array} [argPos] The argument positions of the new function. + * @param {number} [ary] The arity cap of `func`. + * @param {number} [arity] The arity of `func`. + * @returns {Function} Returns the new wrapped function. + */ + function createRecurry(func, bitmask, wrapFunc, placeholder, thisArg, partials, holders, argPos, ary, arity) { + var isCurry = bitmask & WRAP_CURRY_FLAG, + newHolders = isCurry ? holders : undefined, + newHoldersRight = isCurry ? undefined : holders, + newPartials = isCurry ? partials : undefined, + newPartialsRight = isCurry ? undefined : partials; + + bitmask |= (isCurry ? WRAP_PARTIAL_FLAG : WRAP_PARTIAL_RIGHT_FLAG); + bitmask &= ~(isCurry ? WRAP_PARTIAL_RIGHT_FLAG : WRAP_PARTIAL_FLAG); + + if (!(bitmask & WRAP_CURRY_BOUND_FLAG)) { + bitmask &= ~(WRAP_BIND_FLAG | WRAP_BIND_KEY_FLAG); + } + var newData = [ + func, bitmask, thisArg, newPartials, newHolders, newPartialsRight, + newHoldersRight, argPos, ary, arity + ]; + + var result = wrapFunc.apply(undefined, newData); + if (isLaziable(func)) { + setData(result, newData); + } + result.placeholder = placeholder; + return setWrapToString(result, func, bitmask); + } + + /** + * Creates a function like `_.round`. + * + * @private + * @param {string} methodName The name of the `Math` method to use when rounding. + * @returns {Function} Returns the new round function. + */ + function createRound(methodName) { + var func = Math[methodName]; + return function(number, precision) { + number = toNumber(number); + precision = precision == null ? 0 : nativeMin(toInteger(precision), 292); + if (precision && nativeIsFinite(number)) { + // Shift with exponential notation to avoid floating-point issues. + // See [MDN](https://mdn.io/round#Examples) for more details. + var pair = (toString(number) + 'e').split('e'), + value = func(pair[0] + 'e' + (+pair[1] + precision)); + + pair = (toString(value) + 'e').split('e'); + return +(pair[0] + 'e' + (+pair[1] - precision)); + } + return func(number); + }; + } + + /** + * Creates a set object of `values`. + * + * @private + * @param {Array} values The values to add to the set. + * @returns {Object} Returns the new set. + */ + var createSet = !(Set && (1 / setToArray(new Set([,-0]))[1]) == INFINITY) ? noop : function(values) { + return new Set(values); + }; + + /** + * Creates a `_.toPairs` or `_.toPairsIn` function. + * + * @private + * @param {Function} keysFunc The function to get the keys of a given object. + * @returns {Function} Returns the new pairs function. + */ + function createToPairs(keysFunc) { + return function(object) { + var tag = getTag(object); + if (tag == mapTag) { + return mapToArray(object); + } + if (tag == setTag) { + return setToPairs(object); + } + return baseToPairs(object, keysFunc(object)); + }; + } + + /** + * Creates a function that either curries or invokes `func` with optional + * `this` binding and partially applied arguments. + * + * @private + * @param {Function|string} func The function or method name to wrap. + * @param {number} bitmask The bitmask flags. + * 1 - `_.bind` + * 2 - `_.bindKey` + * 4 - `_.curry` or `_.curryRight` of a bound function + * 8 - `_.curry` + * 16 - `_.curryRight` + * 32 - `_.partial` + * 64 - `_.partialRight` + * 128 - `_.rearg` + * 256 - `_.ary` + * 512 - `_.flip` + * @param {*} [thisArg] The `this` binding of `func`. + * @param {Array} [partials] The arguments to be partially applied. + * @param {Array} [holders] The `partials` placeholder indexes. + * @param {Array} [argPos] The argument positions of the new function. + * @param {number} [ary] The arity cap of `func`. + * @param {number} [arity] The arity of `func`. + * @returns {Function} Returns the new wrapped function. + */ + function createWrap(func, bitmask, thisArg, partials, holders, argPos, ary, arity) { + var isBindKey = bitmask & WRAP_BIND_KEY_FLAG; + if (!isBindKey && typeof func != 'function') { + throw new TypeError(FUNC_ERROR_TEXT); + } + var length = partials ? partials.length : 0; + if (!length) { + bitmask &= ~(WRAP_PARTIAL_FLAG | WRAP_PARTIAL_RIGHT_FLAG); + partials = holders = undefined; + } + ary = ary === undefined ? ary : nativeMax(toInteger(ary), 0); + arity = arity === undefined ? arity : toInteger(arity); + length -= holders ? holders.length : 0; + + if (bitmask & WRAP_PARTIAL_RIGHT_FLAG) { + var partialsRight = partials, + holdersRight = holders; + + partials = holders = undefined; + } + var data = isBindKey ? undefined : getData(func); + + var newData = [ + func, bitmask, thisArg, partials, holders, partialsRight, holdersRight, + argPos, ary, arity + ]; + + if (data) { + mergeData(newData, data); + } + func = newData[0]; + bitmask = newData[1]; + thisArg = newData[2]; + partials = newData[3]; + holders = newData[4]; + arity = newData[9] = newData[9] === undefined + ? (isBindKey ? 0 : func.length) + : nativeMax(newData[9] - length, 0); + + if (!arity && bitmask & (WRAP_CURRY_FLAG | WRAP_CURRY_RIGHT_FLAG)) { + bitmask &= ~(WRAP_CURRY_FLAG | WRAP_CURRY_RIGHT_FLAG); + } + if (!bitmask || bitmask == WRAP_BIND_FLAG) { + var result = createBind(func, bitmask, thisArg); + } else if (bitmask == WRAP_CURRY_FLAG || bitmask == WRAP_CURRY_RIGHT_FLAG) { + result = createCurry(func, bitmask, arity); + } else if ((bitmask == WRAP_PARTIAL_FLAG || bitmask == (WRAP_BIND_FLAG | WRAP_PARTIAL_FLAG)) && !holders.length) { + result = createPartial(func, bitmask, thisArg, partials); + } else { + result = createHybrid.apply(undefined, newData); + } + var setter = data ? baseSetData : setData; + return setWrapToString(setter(result, newData), func, bitmask); + } + + /** + * Used by `_.defaults` to customize its `_.assignIn` use to assign properties + * of source objects to the destination object for all destination properties + * that resolve to `undefined`. + * + * @private + * @param {*} objValue The destination value. + * @param {*} srcValue The source value. + * @param {string} key The key of the property to assign. + * @param {Object} object The parent object of `objValue`. + * @returns {*} Returns the value to assign. + */ + function customDefaultsAssignIn(objValue, srcValue, key, object) { + if (objValue === undefined || + (eq(objValue, objectProto[key]) && !hasOwnProperty.call(object, key))) { + return srcValue; + } + return objValue; + } + + /** + * Used by `_.defaultsDeep` to customize its `_.merge` use to merge source + * objects into destination objects that are passed thru. + * + * @private + * @param {*} objValue The destination value. + * @param {*} srcValue The source value. + * @param {string} key The key of the property to merge. + * @param {Object} object The parent object of `objValue`. + * @param {Object} source The parent object of `srcValue`. + * @param {Object} [stack] Tracks traversed source values and their merged + * counterparts. + * @returns {*} Returns the value to assign. + */ + function customDefaultsMerge(objValue, srcValue, key, object, source, stack) { + if (isObject(objValue) && isObject(srcValue)) { + // Recursively merge objects and arrays (susceptible to call stack limits). + stack.set(srcValue, objValue); + baseMerge(objValue, srcValue, undefined, customDefaultsMerge, stack); + stack['delete'](srcValue); + } + return objValue; + } + + /** + * Used by `_.omit` to customize its `_.cloneDeep` use to only clone plain + * objects. + * + * @private + * @param {*} value The value to inspect. + * @param {string} key The key of the property to inspect. + * @returns {*} Returns the uncloned value or `undefined` to defer cloning to `_.cloneDeep`. + */ + function customOmitClone(value) { + return isPlainObject(value) ? undefined : value; + } + + /** + * A specialized version of `baseIsEqualDeep` for arrays with support for + * partial deep comparisons. + * + * @private + * @param {Array} array The array to compare. + * @param {Array} other The other array to compare. + * @param {number} bitmask The bitmask flags. See `baseIsEqual` for more details. + * @param {Function} customizer The function to customize comparisons. + * @param {Function} equalFunc The function to determine equivalents of values. + * @param {Object} stack Tracks traversed `array` and `other` objects. + * @returns {boolean} Returns `true` if the arrays are equivalent, else `false`. + */ + function equalArrays(array, other, bitmask, customizer, equalFunc, stack) { + var isPartial = bitmask & COMPARE_PARTIAL_FLAG, + arrLength = array.length, + othLength = other.length; + + if (arrLength != othLength && !(isPartial && othLength > arrLength)) { + return false; + } + // Check that cyclic values are equal. + var arrStacked = stack.get(array); + var othStacked = stack.get(other); + if (arrStacked && othStacked) { + return arrStacked == other && othStacked == array; + } + var index = -1, + result = true, + seen = (bitmask & COMPARE_UNORDERED_FLAG) ? new SetCache : undefined; + + stack.set(array, other); + stack.set(other, array); + + // Ignore non-index properties. + while (++index < arrLength) { + var arrValue = array[index], + othValue = other[index]; + + if (customizer) { + var compared = isPartial + ? customizer(othValue, arrValue, index, other, array, stack) + : customizer(arrValue, othValue, index, array, other, stack); + } + if (compared !== undefined) { + if (compared) { + continue; + } + result = false; + break; + } + // Recursively compare arrays (susceptible to call stack limits). + if (seen) { + if (!arraySome(other, function(othValue, othIndex) { + if (!cacheHas(seen, othIndex) && + (arrValue === othValue || equalFunc(arrValue, othValue, bitmask, customizer, stack))) { + return seen.push(othIndex); + } + })) { + result = false; + break; + } + } else if (!( + arrValue === othValue || + equalFunc(arrValue, othValue, bitmask, customizer, stack) + )) { + result = false; + break; + } + } + stack['delete'](array); + stack['delete'](other); + return result; + } + + /** + * A specialized version of `baseIsEqualDeep` for comparing objects of + * the same `toStringTag`. + * + * **Note:** This function only supports comparing values with tags of + * `Boolean`, `Date`, `Error`, `Number`, `RegExp`, or `String`. + * + * @private + * @param {Object} object The object to compare. + * @param {Object} other The other object to compare. + * @param {string} tag The `toStringTag` of the objects to compare. + * @param {number} bitmask The bitmask flags. See `baseIsEqual` for more details. + * @param {Function} customizer The function to customize comparisons. + * @param {Function} equalFunc The function to determine equivalents of values. + * @param {Object} stack Tracks traversed `object` and `other` objects. + * @returns {boolean} Returns `true` if the objects are equivalent, else `false`. + */ + function equalByTag(object, other, tag, bitmask, customizer, equalFunc, stack) { + switch (tag) { + case dataViewTag: + if ((object.byteLength != other.byteLength) || + (object.byteOffset != other.byteOffset)) { + return false; + } + object = object.buffer; + other = other.buffer; + + case arrayBufferTag: + if ((object.byteLength != other.byteLength) || + !equalFunc(new Uint8Array(object), new Uint8Array(other))) { + return false; + } + return true; + + case boolTag: + case dateTag: + case numberTag: + // Coerce booleans to `1` or `0` and dates to milliseconds. + // Invalid dates are coerced to `NaN`. + return eq(+object, +other); + + case errorTag: + return object.name == other.name && object.message == other.message; + + case regexpTag: + case stringTag: + // Coerce regexes to strings and treat strings, primitives and objects, + // as equal. See http://www.ecma-international.org/ecma-262/7.0/#sec-regexp.prototype.tostring + // for more details. + return object == (other + ''); + + case mapTag: + var convert = mapToArray; + + case setTag: + var isPartial = bitmask & COMPARE_PARTIAL_FLAG; + convert || (convert = setToArray); + + if (object.size != other.size && !isPartial) { + return false; + } + // Assume cyclic values are equal. + var stacked = stack.get(object); + if (stacked) { + return stacked == other; + } + bitmask |= COMPARE_UNORDERED_FLAG; + + // Recursively compare objects (susceptible to call stack limits). + stack.set(object, other); + var result = equalArrays(convert(object), convert(other), bitmask, customizer, equalFunc, stack); + stack['delete'](object); + return result; + + case symbolTag: + if (symbolValueOf) { + return symbolValueOf.call(object) == symbolValueOf.call(other); + } + } + return false; + } + + /** + * A specialized version of `baseIsEqualDeep` for objects with support for + * partial deep comparisons. + * + * @private + * @param {Object} object The object to compare. + * @param {Object} other The other object to compare. + * @param {number} bitmask The bitmask flags. See `baseIsEqual` for more details. + * @param {Function} customizer The function to customize comparisons. + * @param {Function} equalFunc The function to determine equivalents of values. + * @param {Object} stack Tracks traversed `object` and `other` objects. + * @returns {boolean} Returns `true` if the objects are equivalent, else `false`. + */ + function equalObjects(object, other, bitmask, customizer, equalFunc, stack) { + var isPartial = bitmask & COMPARE_PARTIAL_FLAG, + objProps = getAllKeys(object), + objLength = objProps.length, + othProps = getAllKeys(other), + othLength = othProps.length; + + if (objLength != othLength && !isPartial) { + return false; + } + var index = objLength; + while (index--) { + var key = objProps[index]; + if (!(isPartial ? key in other : hasOwnProperty.call(other, key))) { + return false; + } + } + // Check that cyclic values are equal. + var objStacked = stack.get(object); + var othStacked = stack.get(other); + if (objStacked && othStacked) { + return objStacked == other && othStacked == object; + } + var result = true; + stack.set(object, other); + stack.set(other, object); + + var skipCtor = isPartial; + while (++index < objLength) { + key = objProps[index]; + var objValue = object[key], + othValue = other[key]; + + if (customizer) { + var compared = isPartial + ? customizer(othValue, objValue, key, other, object, stack) + : customizer(objValue, othValue, key, object, other, stack); + } + // Recursively compare objects (susceptible to call stack limits). + if (!(compared === undefined + ? (objValue === othValue || equalFunc(objValue, othValue, bitmask, customizer, stack)) + : compared + )) { + result = false; + break; + } + skipCtor || (skipCtor = key == 'constructor'); + } + if (result && !skipCtor) { + var objCtor = object.constructor, + othCtor = other.constructor; + + // Non `Object` object instances with different constructors are not equal. + if (objCtor != othCtor && + ('constructor' in object && 'constructor' in other) && + !(typeof objCtor == 'function' && objCtor instanceof objCtor && + typeof othCtor == 'function' && othCtor instanceof othCtor)) { + result = false; + } + } + stack['delete'](object); + stack['delete'](other); + return result; + } + + /** + * A specialized version of `baseRest` which flattens the rest array. + * + * @private + * @param {Function} func The function to apply a rest parameter to. + * @returns {Function} Returns the new function. + */ + function flatRest(func) { + return setToString(overRest(func, undefined, flatten), func + ''); + } + + /** + * Creates an array of own enumerable property names and symbols of `object`. + * + * @private + * @param {Object} object The object to query. + * @returns {Array} Returns the array of property names and symbols. + */ + function getAllKeys(object) { + return baseGetAllKeys(object, keys, getSymbols); + } + + /** + * Creates an array of own and inherited enumerable property names and + * symbols of `object`. + * + * @private + * @param {Object} object The object to query. + * @returns {Array} Returns the array of property names and symbols. + */ + function getAllKeysIn(object) { + return baseGetAllKeys(object, keysIn, getSymbolsIn); + } + + /** + * Gets metadata for `func`. + * + * @private + * @param {Function} func The function to query. + * @returns {*} Returns the metadata for `func`. + */ + var getData = !metaMap ? noop : function(func) { + return metaMap.get(func); + }; + + /** + * Gets the name of `func`. + * + * @private + * @param {Function} func The function to query. + * @returns {string} Returns the function name. + */ + function getFuncName(func) { + var result = (func.name + ''), + array = realNames[result], + length = hasOwnProperty.call(realNames, result) ? array.length : 0; + + while (length--) { + var data = array[length], + otherFunc = data.func; + if (otherFunc == null || otherFunc == func) { + return data.name; + } + } + return result; + } + + /** + * Gets the argument placeholder value for `func`. + * + * @private + * @param {Function} func The function to inspect. + * @returns {*} Returns the placeholder value. + */ + function getHolder(func) { + var object = hasOwnProperty.call(lodash, 'placeholder') ? lodash : func; + return object.placeholder; + } + + /** + * Gets the appropriate "iteratee" function. If `_.iteratee` is customized, + * this function returns the custom method, otherwise it returns `baseIteratee`. + * If arguments are provided, the chosen function is invoked with them and + * its result is returned. + * + * @private + * @param {*} [value] The value to convert to an iteratee. + * @param {number} [arity] The arity of the created iteratee. + * @returns {Function} Returns the chosen function or its result. + */ + function getIteratee() { + var result = lodash.iteratee || iteratee; + result = result === iteratee ? baseIteratee : result; + return arguments.length ? result(arguments[0], arguments[1]) : result; + } + + /** + * Gets the data for `map`. + * + * @private + * @param {Object} map The map to query. + * @param {string} key The reference key. + * @returns {*} Returns the map data. + */ + function getMapData(map, key) { + var data = map.__data__; + return isKeyable(key) + ? data[typeof key == 'string' ? 'string' : 'hash'] + : data.map; + } + + /** + * Gets the property names, values, and compare flags of `object`. + * + * @private + * @param {Object} object The object to query. + * @returns {Array} Returns the match data of `object`. + */ + function getMatchData(object) { + var result = keys(object), + length = result.length; + + while (length--) { + var key = result[length], + value = object[key]; + + result[length] = [key, value, isStrictComparable(value)]; + } + return result; + } + + /** + * Gets the native function at `key` of `object`. + * + * @private + * @param {Object} object The object to query. + * @param {string} key The key of the method to get. + * @returns {*} Returns the function if it's native, else `undefined`. + */ + function getNative(object, key) { + var value = getValue(object, key); + return baseIsNative(value) ? value : undefined; + } + + /** + * A specialized version of `baseGetTag` which ignores `Symbol.toStringTag` values. + * + * @private + * @param {*} value The value to query. + * @returns {string} Returns the raw `toStringTag`. + */ + function getRawTag(value) { + var isOwn = hasOwnProperty.call(value, symToStringTag), + tag = value[symToStringTag]; + + try { + value[symToStringTag] = undefined; + var unmasked = true; + } catch (e) {} + + var result = nativeObjectToString.call(value); + if (unmasked) { + if (isOwn) { + value[symToStringTag] = tag; + } else { + delete value[symToStringTag]; + } + } + return result; + } + + /** + * Creates an array of the own enumerable symbols of `object`. + * + * @private + * @param {Object} object The object to query. + * @returns {Array} Returns the array of symbols. + */ + var getSymbols = !nativeGetSymbols ? stubArray : function(object) { + if (object == null) { + return []; + } + object = Object(object); + return arrayFilter(nativeGetSymbols(object), function(symbol) { + return propertyIsEnumerable.call(object, symbol); + }); + }; + + /** + * Creates an array of the own and inherited enumerable symbols of `object`. + * + * @private + * @param {Object} object The object to query. + * @returns {Array} Returns the array of symbols. + */ + var getSymbolsIn = !nativeGetSymbols ? stubArray : function(object) { + var result = []; + while (object) { + arrayPush(result, getSymbols(object)); + object = getPrototype(object); + } + return result; + }; + + /** + * Gets the `toStringTag` of `value`. + * + * @private + * @param {*} value The value to query. + * @returns {string} Returns the `toStringTag`. + */ + var getTag = baseGetTag; + + // Fallback for data views, maps, sets, and weak maps in IE 11 and promises in Node.js < 6. + if ((DataView && getTag(new DataView(new ArrayBuffer(1))) != dataViewTag) || + (Map && getTag(new Map) != mapTag) || + (Promise && getTag(Promise.resolve()) != promiseTag) || + (Set && getTag(new Set) != setTag) || + (WeakMap && getTag(new WeakMap) != weakMapTag)) { + getTag = function(value) { + var result = baseGetTag(value), + Ctor = result == objectTag ? value.constructor : undefined, + ctorString = Ctor ? toSource(Ctor) : ''; + + if (ctorString) { + switch (ctorString) { + case dataViewCtorString: return dataViewTag; + case mapCtorString: return mapTag; + case promiseCtorString: return promiseTag; + case setCtorString: return setTag; + case weakMapCtorString: return weakMapTag; + } + } + return result; + }; + } + + /** + * Gets the view, applying any `transforms` to the `start` and `end` positions. + * + * @private + * @param {number} start The start of the view. + * @param {number} end The end of the view. + * @param {Array} transforms The transformations to apply to the view. + * @returns {Object} Returns an object containing the `start` and `end` + * positions of the view. + */ + function getView(start, end, transforms) { + var index = -1, + length = transforms.length; + + while (++index < length) { + var data = transforms[index], + size = data.size; + + switch (data.type) { + case 'drop': start += size; break; + case 'dropRight': end -= size; break; + case 'take': end = nativeMin(end, start + size); break; + case 'takeRight': start = nativeMax(start, end - size); break; + } + } + return { 'start': start, 'end': end }; + } + + /** + * Extracts wrapper details from the `source` body comment. + * + * @private + * @param {string} source The source to inspect. + * @returns {Array} Returns the wrapper details. + */ + function getWrapDetails(source) { + var match = source.match(reWrapDetails); + return match ? match[1].split(reSplitDetails) : []; + } + + /** + * Checks if `path` exists on `object`. + * + * @private + * @param {Object} object The object to query. + * @param {Array|string} path The path to check. + * @param {Function} hasFunc The function to check properties. + * @returns {boolean} Returns `true` if `path` exists, else `false`. + */ + function hasPath(object, path, hasFunc) { + path = castPath(path, object); + + var index = -1, + length = path.length, + result = false; + + while (++index < length) { + var key = toKey(path[index]); + if (!(result = object != null && hasFunc(object, key))) { + break; + } + object = object[key]; + } + if (result || ++index != length) { + return result; + } + length = object == null ? 0 : object.length; + return !!length && isLength(length) && isIndex(key, length) && + (isArray(object) || isArguments(object)); + } + + /** + * Initializes an array clone. + * + * @private + * @param {Array} array The array to clone. + * @returns {Array} Returns the initialized clone. + */ + function initCloneArray(array) { + var length = array.length, + result = new array.constructor(length); + + // Add properties assigned by `RegExp#exec`. + if (length && typeof array[0] == 'string' && hasOwnProperty.call(array, 'index')) { + result.index = array.index; + result.input = array.input; + } + return result; + } + + /** + * Initializes an object clone. + * + * @private + * @param {Object} object The object to clone. + * @returns {Object} Returns the initialized clone. + */ + function initCloneObject(object) { + return (typeof object.constructor == 'function' && !isPrototype(object)) + ? baseCreate(getPrototype(object)) + : {}; + } + + /** + * Initializes an object clone based on its `toStringTag`. + * + * **Note:** This function only supports cloning values with tags of + * `Boolean`, `Date`, `Error`, `Map`, `Number`, `RegExp`, `Set`, or `String`. + * + * @private + * @param {Object} object The object to clone. + * @param {string} tag The `toStringTag` of the object to clone. + * @param {boolean} [isDeep] Specify a deep clone. + * @returns {Object} Returns the initialized clone. + */ + function initCloneByTag(object, tag, isDeep) { + var Ctor = object.constructor; + switch (tag) { + case arrayBufferTag: + return cloneArrayBuffer(object); + + case boolTag: + case dateTag: + return new Ctor(+object); + + case dataViewTag: + return cloneDataView(object, isDeep); + + case float32Tag: case float64Tag: + case int8Tag: case int16Tag: case int32Tag: + case uint8Tag: case uint8ClampedTag: case uint16Tag: case uint32Tag: + return cloneTypedArray(object, isDeep); + + case mapTag: + return new Ctor; + + case numberTag: + case stringTag: + return new Ctor(object); + + case regexpTag: + return cloneRegExp(object); + + case setTag: + return new Ctor; + + case symbolTag: + return cloneSymbol(object); + } + } + + /** + * Inserts wrapper `details` in a comment at the top of the `source` body. + * + * @private + * @param {string} source The source to modify. + * @returns {Array} details The details to insert. + * @returns {string} Returns the modified source. + */ + function insertWrapDetails(source, details) { + var length = details.length; + if (!length) { + return source; + } + var lastIndex = length - 1; + details[lastIndex] = (length > 1 ? '& ' : '') + details[lastIndex]; + details = details.join(length > 2 ? ', ' : ' '); + return source.replace(reWrapComment, '{\n/* [wrapped with ' + details + '] */\n'); + } + + /** + * Checks if `value` is a flattenable `arguments` object or array. + * + * @private + * @param {*} value The value to check. + * @returns {boolean} Returns `true` if `value` is flattenable, else `false`. + */ + function isFlattenable(value) { + return isArray(value) || isArguments(value) || + !!(spreadableSymbol && value && value[spreadableSymbol]); + } + + /** + * Checks if `value` is a valid array-like index. + * + * @private + * @param {*} value The value to check. + * @param {number} [length=MAX_SAFE_INTEGER] The upper bounds of a valid index. + * @returns {boolean} Returns `true` if `value` is a valid index, else `false`. + */ + function isIndex(value, length) { + var type = typeof value; + length = length == null ? MAX_SAFE_INTEGER : length; + + return !!length && + (type == 'number' || + (type != 'symbol' && reIsUint.test(value))) && + (value > -1 && value % 1 == 0 && value < length); + } + + /** + * Checks if the given arguments are from an iteratee call. + * + * @private + * @param {*} value The potential iteratee value argument. + * @param {*} index The potential iteratee index or key argument. + * @param {*} object The potential iteratee object argument. + * @returns {boolean} Returns `true` if the arguments are from an iteratee call, + * else `false`. + */ + function isIterateeCall(value, index, object) { + if (!isObject(object)) { + return false; + } + var type = typeof index; + if (type == 'number' + ? (isArrayLike(object) && isIndex(index, object.length)) + : (type == 'string' && index in object) + ) { + return eq(object[index], value); + } + return false; + } + + /** + * Checks if `value` is a property name and not a property path. + * + * @private + * @param {*} value The value to check. + * @param {Object} [object] The object to query keys on. + * @returns {boolean} Returns `true` if `value` is a property name, else `false`. + */ + function isKey(value, object) { + if (isArray(value)) { + return false; + } + var type = typeof value; + if (type == 'number' || type == 'symbol' || type == 'boolean' || + value == null || isSymbol(value)) { + return true; + } + return reIsPlainProp.test(value) || !reIsDeepProp.test(value) || + (object != null && value in Object(object)); + } + + /** + * Checks if `value` is suitable for use as unique object key. + * + * @private + * @param {*} value The value to check. + * @returns {boolean} Returns `true` if `value` is suitable, else `false`. + */ + function isKeyable(value) { + var type = typeof value; + return (type == 'string' || type == 'number' || type == 'symbol' || type == 'boolean') + ? (value !== '__proto__') + : (value === null); + } + + /** + * Checks if `func` has a lazy counterpart. + * + * @private + * @param {Function} func The function to check. + * @returns {boolean} Returns `true` if `func` has a lazy counterpart, + * else `false`. + */ + function isLaziable(func) { + var funcName = getFuncName(func), + other = lodash[funcName]; + + if (typeof other != 'function' || !(funcName in LazyWrapper.prototype)) { + return false; + } + if (func === other) { + return true; + } + var data = getData(other); + return !!data && func === data[0]; + } + + /** + * Checks if `func` has its source masked. + * + * @private + * @param {Function} func The function to check. + * @returns {boolean} Returns `true` if `func` is masked, else `false`. + */ + function isMasked(func) { + return !!maskSrcKey && (maskSrcKey in func); + } + + /** + * Checks if `func` is capable of being masked. + * + * @private + * @param {*} value The value to check. + * @returns {boolean} Returns `true` if `func` is maskable, else `false`. + */ + var isMaskable = coreJsData ? isFunction : stubFalse; + + /** + * Checks if `value` is likely a prototype object. + * + * @private + * @param {*} value The value to check. + * @returns {boolean} Returns `true` if `value` is a prototype, else `false`. + */ + function isPrototype(value) { + var Ctor = value && value.constructor, + proto = (typeof Ctor == 'function' && Ctor.prototype) || objectProto; + + return value === proto; + } + + /** + * Checks if `value` is suitable for strict equality comparisons, i.e. `===`. + * + * @private + * @param {*} value The value to check. + * @returns {boolean} Returns `true` if `value` if suitable for strict + * equality comparisons, else `false`. + */ + function isStrictComparable(value) { + return value === value && !isObject(value); + } + + /** + * A specialized version of `matchesProperty` for source values suitable + * for strict equality comparisons, i.e. `===`. + * + * @private + * @param {string} key The key of the property to get. + * @param {*} srcValue The value to match. + * @returns {Function} Returns the new spec function. + */ + function matchesStrictComparable(key, srcValue) { + return function(object) { + if (object == null) { + return false; + } + return object[key] === srcValue && + (srcValue !== undefined || (key in Object(object))); + }; + } + + /** + * A specialized version of `_.memoize` which clears the memoized function's + * cache when it exceeds `MAX_MEMOIZE_SIZE`. + * + * @private + * @param {Function} func The function to have its output memoized. + * @returns {Function} Returns the new memoized function. + */ + function memoizeCapped(func) { + var result = memoize(func, function(key) { + if (cache.size === MAX_MEMOIZE_SIZE) { + cache.clear(); + } + return key; + }); + + var cache = result.cache; + return result; + } + + /** + * Merges the function metadata of `source` into `data`. + * + * Merging metadata reduces the number of wrappers used to invoke a function. + * This is possible because methods like `_.bind`, `_.curry`, and `_.partial` + * may be applied regardless of execution order. Methods like `_.ary` and + * `_.rearg` modify function arguments, making the order in which they are + * executed important, preventing the merging of metadata. However, we make + * an exception for a safe combined case where curried functions have `_.ary` + * and or `_.rearg` applied. + * + * @private + * @param {Array} data The destination metadata. + * @param {Array} source The source metadata. + * @returns {Array} Returns `data`. + */ + function mergeData(data, source) { + var bitmask = data[1], + srcBitmask = source[1], + newBitmask = bitmask | srcBitmask, + isCommon = newBitmask < (WRAP_BIND_FLAG | WRAP_BIND_KEY_FLAG | WRAP_ARY_FLAG); + + var isCombo = + ((srcBitmask == WRAP_ARY_FLAG) && (bitmask == WRAP_CURRY_FLAG)) || + ((srcBitmask == WRAP_ARY_FLAG) && (bitmask == WRAP_REARG_FLAG) && (data[7].length <= source[8])) || + ((srcBitmask == (WRAP_ARY_FLAG | WRAP_REARG_FLAG)) && (source[7].length <= source[8]) && (bitmask == WRAP_CURRY_FLAG)); + + // Exit early if metadata can't be merged. + if (!(isCommon || isCombo)) { + return data; + } + // Use source `thisArg` if available. + if (srcBitmask & WRAP_BIND_FLAG) { + data[2] = source[2]; + // Set when currying a bound function. + newBitmask |= bitmask & WRAP_BIND_FLAG ? 0 : WRAP_CURRY_BOUND_FLAG; + } + // Compose partial arguments. + var value = source[3]; + if (value) { + var partials = data[3]; + data[3] = partials ? composeArgs(partials, value, source[4]) : value; + data[4] = partials ? replaceHolders(data[3], PLACEHOLDER) : source[4]; + } + // Compose partial right arguments. + value = source[5]; + if (value) { + partials = data[5]; + data[5] = partials ? composeArgsRight(partials, value, source[6]) : value; + data[6] = partials ? replaceHolders(data[5], PLACEHOLDER) : source[6]; + } + // Use source `argPos` if available. + value = source[7]; + if (value) { + data[7] = value; + } + // Use source `ary` if it's smaller. + if (srcBitmask & WRAP_ARY_FLAG) { + data[8] = data[8] == null ? source[8] : nativeMin(data[8], source[8]); + } + // Use source `arity` if one is not provided. + if (data[9] == null) { + data[9] = source[9]; + } + // Use source `func` and merge bitmasks. + data[0] = source[0]; + data[1] = newBitmask; + + return data; + } + + /** + * This function is like + * [`Object.keys`](http://ecma-international.org/ecma-262/7.0/#sec-object.keys) + * except that it includes inherited enumerable properties. + * + * @private + * @param {Object} object The object to query. + * @returns {Array} Returns the array of property names. + */ + function nativeKeysIn(object) { + var result = []; + if (object != null) { + for (var key in Object(object)) { + result.push(key); + } + } + return result; + } + + /** + * Converts `value` to a string using `Object.prototype.toString`. + * + * @private + * @param {*} value The value to convert. + * @returns {string} Returns the converted string. + */ + function objectToString(value) { + return nativeObjectToString.call(value); + } + + /** + * A specialized version of `baseRest` which transforms the rest array. + * + * @private + * @param {Function} func The function to apply a rest parameter to. + * @param {number} [start=func.length-1] The start position of the rest parameter. + * @param {Function} transform The rest array transform. + * @returns {Function} Returns the new function. + */ + function overRest(func, start, transform) { + start = nativeMax(start === undefined ? (func.length - 1) : start, 0); + return function() { + var args = arguments, + index = -1, + length = nativeMax(args.length - start, 0), + array = Array(length); + + while (++index < length) { + array[index] = args[start + index]; + } + index = -1; + var otherArgs = Array(start + 1); + while (++index < start) { + otherArgs[index] = args[index]; + } + otherArgs[start] = transform(array); + return apply(func, this, otherArgs); + }; + } + + /** + * Gets the parent value at `path` of `object`. + * + * @private + * @param {Object} object The object to query. + * @param {Array} path The path to get the parent value of. + * @returns {*} Returns the parent value. + */ + function parent(object, path) { + return path.length < 2 ? object : baseGet(object, baseSlice(path, 0, -1)); + } + + /** + * Reorder `array` according to the specified indexes where the element at + * the first index is assigned as the first element, the element at + * the second index is assigned as the second element, and so on. + * + * @private + * @param {Array} array The array to reorder. + * @param {Array} indexes The arranged array indexes. + * @returns {Array} Returns `array`. + */ + function reorder(array, indexes) { + var arrLength = array.length, + length = nativeMin(indexes.length, arrLength), + oldArray = copyArray(array); + + while (length--) { + var index = indexes[length]; + array[length] = isIndex(index, arrLength) ? oldArray[index] : undefined; + } + return array; + } + + /** + * Gets the value at `key`, unless `key` is "__proto__" or "constructor". + * + * @private + * @param {Object} object The object to query. + * @param {string} key The key of the property to get. + * @returns {*} Returns the property value. + */ + function safeGet(object, key) { + if (key === 'constructor' && typeof object[key] === 'function') { + return; + } + + if (key == '__proto__') { + return; + } + + return object[key]; + } + + /** + * Sets metadata for `func`. + * + * **Note:** If this function becomes hot, i.e. is invoked a lot in a short + * period of time, it will trip its breaker and transition to an identity + * function to avoid garbage collection pauses in V8. See + * [V8 issue 2070](https://bugs.chromium.org/p/v8/issues/detail?id=2070) + * for more details. + * + * @private + * @param {Function} func The function to associate metadata with. + * @param {*} data The metadata. + * @returns {Function} Returns `func`. + */ + var setData = shortOut(baseSetData); + + /** + * A simple wrapper around the global [`setTimeout`](https://mdn.io/setTimeout). + * + * @private + * @param {Function} func The function to delay. + * @param {number} wait The number of milliseconds to delay invocation. + * @returns {number|Object} Returns the timer id or timeout object. + */ + var setTimeout = ctxSetTimeout || function(func, wait) { + return root.setTimeout(func, wait); + }; + + /** + * Sets the `toString` method of `func` to return `string`. + * + * @private + * @param {Function} func The function to modify. + * @param {Function} string The `toString` result. + * @returns {Function} Returns `func`. + */ + var setToString = shortOut(baseSetToString); + + /** + * Sets the `toString` method of `wrapper` to mimic the source of `reference` + * with wrapper details in a comment at the top of the source body. + * + * @private + * @param {Function} wrapper The function to modify. + * @param {Function} reference The reference function. + * @param {number} bitmask The bitmask flags. See `createWrap` for more details. + * @returns {Function} Returns `wrapper`. + */ + function setWrapToString(wrapper, reference, bitmask) { + var source = (reference + ''); + return setToString(wrapper, insertWrapDetails(source, updateWrapDetails(getWrapDetails(source), bitmask))); + } + + /** + * Creates a function that'll short out and invoke `identity` instead + * of `func` when it's called `HOT_COUNT` or more times in `HOT_SPAN` + * milliseconds. + * + * @private + * @param {Function} func The function to restrict. + * @returns {Function} Returns the new shortable function. + */ + function shortOut(func) { + var count = 0, + lastCalled = 0; + + return function() { + var stamp = nativeNow(), + remaining = HOT_SPAN - (stamp - lastCalled); + + lastCalled = stamp; + if (remaining > 0) { + if (++count >= HOT_COUNT) { + return arguments[0]; + } + } else { + count = 0; + } + return func.apply(undefined, arguments); + }; + } + + /** + * A specialized version of `_.shuffle` which mutates and sets the size of `array`. + * + * @private + * @param {Array} array The array to shuffle. + * @param {number} [size=array.length] The size of `array`. + * @returns {Array} Returns `array`. + */ + function shuffleSelf(array, size) { + var index = -1, + length = array.length, + lastIndex = length - 1; + + size = size === undefined ? length : size; + while (++index < size) { + var rand = baseRandom(index, lastIndex), + value = array[rand]; + + array[rand] = array[index]; + array[index] = value; + } + array.length = size; + return array; + } + + /** + * Converts `string` to a property path array. + * + * @private + * @param {string} string The string to convert. + * @returns {Array} Returns the property path array. + */ + var stringToPath = memoizeCapped(function(string) { + var result = []; + if (string.charCodeAt(0) === 46 /* . */) { + result.push(''); + } + string.replace(rePropName, function(match, number, quote, subString) { + result.push(quote ? subString.replace(reEscapeChar, '$1') : (number || match)); + }); + return result; + }); + + /** + * Converts `value` to a string key if it's not a string or symbol. + * + * @private + * @param {*} value The value to inspect. + * @returns {string|symbol} Returns the key. + */ + function toKey(value) { + if (typeof value == 'string' || isSymbol(value)) { + return value; + } + var result = (value + ''); + return (result == '0' && (1 / value) == -INFINITY) ? '-0' : result; + } + + /** + * Converts `func` to its source code. + * + * @private + * @param {Function} func The function to convert. + * @returns {string} Returns the source code. + */ + function toSource(func) { + if (func != null) { + try { + return funcToString.call(func); + } catch (e) {} + try { + return (func + ''); + } catch (e) {} + } + return ''; + } + + /** + * Updates wrapper `details` based on `bitmask` flags. + * + * @private + * @returns {Array} details The details to modify. + * @param {number} bitmask The bitmask flags. See `createWrap` for more details. + * @returns {Array} Returns `details`. + */ + function updateWrapDetails(details, bitmask) { + arrayEach(wrapFlags, function(pair) { + var value = '_.' + pair[0]; + if ((bitmask & pair[1]) && !arrayIncludes(details, value)) { + details.push(value); + } + }); + return details.sort(); + } + + /** + * Creates a clone of `wrapper`. + * + * @private + * @param {Object} wrapper The wrapper to clone. + * @returns {Object} Returns the cloned wrapper. + */ + function wrapperClone(wrapper) { + if (wrapper instanceof LazyWrapper) { + return wrapper.clone(); + } + var result = new LodashWrapper(wrapper.__wrapped__, wrapper.__chain__); + result.__actions__ = copyArray(wrapper.__actions__); + result.__index__ = wrapper.__index__; + result.__values__ = wrapper.__values__; + return result; + } + + /*------------------------------------------------------------------------*/ + + /** + * Creates an array of elements split into groups the length of `size`. + * If `array` can't be split evenly, the final chunk will be the remaining + * elements. + * + * @static + * @memberOf _ + * @since 3.0.0 + * @category Array + * @param {Array} array The array to process. + * @param {number} [size=1] The length of each chunk + * @param- {Object} [guard] Enables use as an iteratee for methods like `_.map`. + * @returns {Array} Returns the new array of chunks. + * @example + * + * _.chunk(['a', 'b', 'c', 'd'], 2); + * // => [['a', 'b'], ['c', 'd']] + * + * _.chunk(['a', 'b', 'c', 'd'], 3); + * // => [['a', 'b', 'c'], ['d']] + */ + function chunk(array, size, guard) { + if ((guard ? isIterateeCall(array, size, guard) : size === undefined)) { + size = 1; + } else { + size = nativeMax(toInteger(size), 0); + } + var length = array == null ? 0 : array.length; + if (!length || size < 1) { + return []; + } + var index = 0, + resIndex = 0, + result = Array(nativeCeil(length / size)); + + while (index < length) { + result[resIndex++] = baseSlice(array, index, (index += size)); + } + return result; + } + + /** + * Creates an array with all falsey values removed. The values `false`, `null`, + * `0`, `""`, `undefined`, and `NaN` are falsey. + * + * @static + * @memberOf _ + * @since 0.1.0 + * @category Array + * @param {Array} array The array to compact. + * @returns {Array} Returns the new array of filtered values. + * @example + * + * _.compact([0, 1, false, 2, '', 3]); + * // => [1, 2, 3] + */ + function compact(array) { + var index = -1, + length = array == null ? 0 : array.length, + resIndex = 0, + result = []; + + while (++index < length) { + var value = array[index]; + if (value) { + result[resIndex++] = value; + } + } + return result; + } + + /** + * Creates a new array concatenating `array` with any additional arrays + * and/or values. + * + * @static + * @memberOf _ + * @since 4.0.0 + * @category Array + * @param {Array} array The array to concatenate. + * @param {...*} [values] The values to concatenate. + * @returns {Array} Returns the new concatenated array. + * @example + * + * var array = [1]; + * var other = _.concat(array, 2, [3], [[4]]); + * + * console.log(other); + * // => [1, 2, 3, [4]] + * + * console.log(array); + * // => [1] + */ + function concat() { + var length = arguments.length; + if (!length) { + return []; + } + var args = Array(length - 1), + array = arguments[0], + index = length; + + while (index--) { + args[index - 1] = arguments[index]; + } + return arrayPush(isArray(array) ? copyArray(array) : [array], baseFlatten(args, 1)); + } + + /** + * Creates an array of `array` values not included in the other given arrays + * using [`SameValueZero`](http://ecma-international.org/ecma-262/7.0/#sec-samevaluezero) + * for equality comparisons. The order and references of result values are + * determined by the first array. + * + * **Note:** Unlike `_.pullAll`, this method returns a new array. + * + * @static + * @memberOf _ + * @since 0.1.0 + * @category Array + * @param {Array} array The array to inspect. + * @param {...Array} [values] The values to exclude. + * @returns {Array} Returns the new array of filtered values. + * @see _.without, _.xor + * @example + * + * _.difference([2, 1], [2, 3]); + * // => [1] + */ + var difference = baseRest(function(array, values) { + return isArrayLikeObject(array) + ? baseDifference(array, baseFlatten(values, 1, isArrayLikeObject, true)) + : []; + }); + + /** + * This method is like `_.difference` except that it accepts `iteratee` which + * is invoked for each element of `array` and `values` to generate the criterion + * by which they're compared. The order and references of result values are + * determined by the first array. The iteratee is invoked with one argument: + * (value). + * + * **Note:** Unlike `_.pullAllBy`, this method returns a new array. + * + * @static + * @memberOf _ + * @since 4.0.0 + * @category Array + * @param {Array} array The array to inspect. + * @param {...Array} [values] The values to exclude. + * @param {Function} [iteratee=_.identity] The iteratee invoked per element. + * @returns {Array} Returns the new array of filtered values. + * @example + * + * _.differenceBy([2.1, 1.2], [2.3, 3.4], Math.floor); + * // => [1.2] + * + * // The `_.property` iteratee shorthand. + * _.differenceBy([{ 'x': 2 }, { 'x': 1 }], [{ 'x': 1 }], 'x'); + * // => [{ 'x': 2 }] + */ + var differenceBy = baseRest(function(array, values) { + var iteratee = last(values); + if (isArrayLikeObject(iteratee)) { + iteratee = undefined; + } + return isArrayLikeObject(array) + ? baseDifference(array, baseFlatten(values, 1, isArrayLikeObject, true), getIteratee(iteratee, 2)) + : []; + }); + + /** + * This method is like `_.difference` except that it accepts `comparator` + * which is invoked to compare elements of `array` to `values`. The order and + * references of result values are determined by the first array. The comparator + * is invoked with two arguments: (arrVal, othVal). + * + * **Note:** Unlike `_.pullAllWith`, this method returns a new array. + * + * @static + * @memberOf _ + * @since 4.0.0 + * @category Array + * @param {Array} array The array to inspect. + * @param {...Array} [values] The values to exclude. + * @param {Function} [comparator] The comparator invoked per element. + * @returns {Array} Returns the new array of filtered values. + * @example + * + * var objects = [{ 'x': 1, 'y': 2 }, { 'x': 2, 'y': 1 }]; + * + * _.differenceWith(objects, [{ 'x': 1, 'y': 2 }], _.isEqual); + * // => [{ 'x': 2, 'y': 1 }] + */ + var differenceWith = baseRest(function(array, values) { + var comparator = last(values); + if (isArrayLikeObject(comparator)) { + comparator = undefined; + } + return isArrayLikeObject(array) + ? baseDifference(array, baseFlatten(values, 1, isArrayLikeObject, true), undefined, comparator) + : []; + }); + + /** + * Creates a slice of `array` with `n` elements dropped from the beginning. + * + * @static + * @memberOf _ + * @since 0.5.0 + * @category Array + * @param {Array} array The array to query. + * @param {number} [n=1] The number of elements to drop. + * @param- {Object} [guard] Enables use as an iteratee for methods like `_.map`. + * @returns {Array} Returns the slice of `array`. + * @example + * + * _.drop([1, 2, 3]); + * // => [2, 3] + * + * _.drop([1, 2, 3], 2); + * // => [3] + * + * _.drop([1, 2, 3], 5); + * // => [] + * + * _.drop([1, 2, 3], 0); + * // => [1, 2, 3] + */ + function drop(array, n, guard) { + var length = array == null ? 0 : array.length; + if (!length) { + return []; + } + n = (guard || n === undefined) ? 1 : toInteger(n); + return baseSlice(array, n < 0 ? 0 : n, length); + } + + /** + * Creates a slice of `array` with `n` elements dropped from the end. + * + * @static + * @memberOf _ + * @since 3.0.0 + * @category Array + * @param {Array} array The array to query. + * @param {number} [n=1] The number of elements to drop. + * @param- {Object} [guard] Enables use as an iteratee for methods like `_.map`. + * @returns {Array} Returns the slice of `array`. + * @example + * + * _.dropRight([1, 2, 3]); + * // => [1, 2] + * + * _.dropRight([1, 2, 3], 2); + * // => [1] + * + * _.dropRight([1, 2, 3], 5); + * // => [] + * + * _.dropRight([1, 2, 3], 0); + * // => [1, 2, 3] + */ + function dropRight(array, n, guard) { + var length = array == null ? 0 : array.length; + if (!length) { + return []; + } + n = (guard || n === undefined) ? 1 : toInteger(n); + n = length - n; + return baseSlice(array, 0, n < 0 ? 0 : n); + } + + /** + * Creates a slice of `array` excluding elements dropped from the end. + * Elements are dropped until `predicate` returns falsey. The predicate is + * invoked with three arguments: (value, index, array). + * + * @static + * @memberOf _ + * @since 3.0.0 + * @category Array + * @param {Array} array The array to query. + * @param {Function} [predicate=_.identity] The function invoked per iteration. + * @returns {Array} Returns the slice of `array`. + * @example + * + * var users = [ + * { 'user': 'barney', 'active': true }, + * { 'user': 'fred', 'active': false }, + * { 'user': 'pebbles', 'active': false } + * ]; + * + * _.dropRightWhile(users, function(o) { return !o.active; }); + * // => objects for ['barney'] + * + * // The `_.matches` iteratee shorthand. + * _.dropRightWhile(users, { 'user': 'pebbles', 'active': false }); + * // => objects for ['barney', 'fred'] + * + * // The `_.matchesProperty` iteratee shorthand. + * _.dropRightWhile(users, ['active', false]); + * // => objects for ['barney'] + * + * // The `_.property` iteratee shorthand. + * _.dropRightWhile(users, 'active'); + * // => objects for ['barney', 'fred', 'pebbles'] + */ + function dropRightWhile(array, predicate) { + return (array && array.length) + ? baseWhile(array, getIteratee(predicate, 3), true, true) + : []; + } + + /** + * Creates a slice of `array` excluding elements dropped from the beginning. + * Elements are dropped until `predicate` returns falsey. The predicate is + * invoked with three arguments: (value, index, array). + * + * @static + * @memberOf _ + * @since 3.0.0 + * @category Array + * @param {Array} array The array to query. + * @param {Function} [predicate=_.identity] The function invoked per iteration. + * @returns {Array} Returns the slice of `array`. + * @example + * + * var users = [ + * { 'user': 'barney', 'active': false }, + * { 'user': 'fred', 'active': false }, + * { 'user': 'pebbles', 'active': true } + * ]; + * + * _.dropWhile(users, function(o) { return !o.active; }); + * // => objects for ['pebbles'] + * + * // The `_.matches` iteratee shorthand. + * _.dropWhile(users, { 'user': 'barney', 'active': false }); + * // => objects for ['fred', 'pebbles'] + * + * // The `_.matchesProperty` iteratee shorthand. + * _.dropWhile(users, ['active', false]); + * // => objects for ['pebbles'] + * + * // The `_.property` iteratee shorthand. + * _.dropWhile(users, 'active'); + * // => objects for ['barney', 'fred', 'pebbles'] + */ + function dropWhile(array, predicate) { + return (array && array.length) + ? baseWhile(array, getIteratee(predicate, 3), true) + : []; + } + + /** + * Fills elements of `array` with `value` from `start` up to, but not + * including, `end`. + * + * **Note:** This method mutates `array`. + * + * @static + * @memberOf _ + * @since 3.2.0 + * @category Array + * @param {Array} array The array to fill. + * @param {*} value The value to fill `array` with. + * @param {number} [start=0] The start position. + * @param {number} [end=array.length] The end position. + * @returns {Array} Returns `array`. + * @example + * + * var array = [1, 2, 3]; + * + * _.fill(array, 'a'); + * console.log(array); + * // => ['a', 'a', 'a'] + * + * _.fill(Array(3), 2); + * // => [2, 2, 2] + * + * _.fill([4, 6, 8, 10], '*', 1, 3); + * // => [4, '*', '*', 10] + */ + function fill(array, value, start, end) { + var length = array == null ? 0 : array.length; + if (!length) { + return []; + } + if (start && typeof start != 'number' && isIterateeCall(array, value, start)) { + start = 0; + end = length; + } + return baseFill(array, value, start, end); + } + + /** + * This method is like `_.find` except that it returns the index of the first + * element `predicate` returns truthy for instead of the element itself. + * + * @static + * @memberOf _ + * @since 1.1.0 + * @category Array + * @param {Array} array The array to inspect. + * @param {Function} [predicate=_.identity] The function invoked per iteration. + * @param {number} [fromIndex=0] The index to search from. + * @returns {number} Returns the index of the found element, else `-1`. + * @example + * + * var users = [ + * { 'user': 'barney', 'active': false }, + * { 'user': 'fred', 'active': false }, + * { 'user': 'pebbles', 'active': true } + * ]; + * + * _.findIndex(users, function(o) { return o.user == 'barney'; }); + * // => 0 + * + * // The `_.matches` iteratee shorthand. + * _.findIndex(users, { 'user': 'fred', 'active': false }); + * // => 1 + * + * // The `_.matchesProperty` iteratee shorthand. + * _.findIndex(users, ['active', false]); + * // => 0 + * + * // The `_.property` iteratee shorthand. + * _.findIndex(users, 'active'); + * // => 2 + */ + function findIndex(array, predicate, fromIndex) { + var length = array == null ? 0 : array.length; + if (!length) { + return -1; + } + var index = fromIndex == null ? 0 : toInteger(fromIndex); + if (index < 0) { + index = nativeMax(length + index, 0); + } + return baseFindIndex(array, getIteratee(predicate, 3), index); + } + + /** + * This method is like `_.findIndex` except that it iterates over elements + * of `collection` from right to left. + * + * @static + * @memberOf _ + * @since 2.0.0 + * @category Array + * @param {Array} array The array to inspect. + * @param {Function} [predicate=_.identity] The function invoked per iteration. + * @param {number} [fromIndex=array.length-1] The index to search from. + * @returns {number} Returns the index of the found element, else `-1`. + * @example + * + * var users = [ + * { 'user': 'barney', 'active': true }, + * { 'user': 'fred', 'active': false }, + * { 'user': 'pebbles', 'active': false } + * ]; + * + * _.findLastIndex(users, function(o) { return o.user == 'pebbles'; }); + * // => 2 + * + * // The `_.matches` iteratee shorthand. + * _.findLastIndex(users, { 'user': 'barney', 'active': true }); + * // => 0 + * + * // The `_.matchesProperty` iteratee shorthand. + * _.findLastIndex(users, ['active', false]); + * // => 2 + * + * // The `_.property` iteratee shorthand. + * _.findLastIndex(users, 'active'); + * // => 0 + */ + function findLastIndex(array, predicate, fromIndex) { + var length = array == null ? 0 : array.length; + if (!length) { + return -1; + } + var index = length - 1; + if (fromIndex !== undefined) { + index = toInteger(fromIndex); + index = fromIndex < 0 + ? nativeMax(length + index, 0) + : nativeMin(index, length - 1); + } + return baseFindIndex(array, getIteratee(predicate, 3), index, true); + } + + /** + * Flattens `array` a single level deep. + * + * @static + * @memberOf _ + * @since 0.1.0 + * @category Array + * @param {Array} array The array to flatten. + * @returns {Array} Returns the new flattened array. + * @example + * + * _.flatten([1, [2, [3, [4]], 5]]); + * // => [1, 2, [3, [4]], 5] + */ + function flatten(array) { + var length = array == null ? 0 : array.length; + return length ? baseFlatten(array, 1) : []; + } + + /** + * Recursively flattens `array`. + * + * @static + * @memberOf _ + * @since 3.0.0 + * @category Array + * @param {Array} array The array to flatten. + * @returns {Array} Returns the new flattened array. + * @example + * + * _.flattenDeep([1, [2, [3, [4]], 5]]); + * // => [1, 2, 3, 4, 5] + */ + function flattenDeep(array) { + var length = array == null ? 0 : array.length; + return length ? baseFlatten(array, INFINITY) : []; + } + + /** + * Recursively flatten `array` up to `depth` times. + * + * @static + * @memberOf _ + * @since 4.4.0 + * @category Array + * @param {Array} array The array to flatten. + * @param {number} [depth=1] The maximum recursion depth. + * @returns {Array} Returns the new flattened array. + * @example + * + * var array = [1, [2, [3, [4]], 5]]; + * + * _.flattenDepth(array, 1); + * // => [1, 2, [3, [4]], 5] + * + * _.flattenDepth(array, 2); + * // => [1, 2, 3, [4], 5] + */ + function flattenDepth(array, depth) { + var length = array == null ? 0 : array.length; + if (!length) { + return []; + } + depth = depth === undefined ? 1 : toInteger(depth); + return baseFlatten(array, depth); + } + + /** + * The inverse of `_.toPairs`; this method returns an object composed + * from key-value `pairs`. + * + * @static + * @memberOf _ + * @since 4.0.0 + * @category Array + * @param {Array} pairs The key-value pairs. + * @returns {Object} Returns the new object. + * @example + * + * _.fromPairs([['a', 1], ['b', 2]]); + * // => { 'a': 1, 'b': 2 } + */ + function fromPairs(pairs) { + var index = -1, + length = pairs == null ? 0 : pairs.length, + result = {}; + + while (++index < length) { + var pair = pairs[index]; + result[pair[0]] = pair[1]; + } + return result; + } + + /** + * Gets the first element of `array`. + * + * @static + * @memberOf _ + * @since 0.1.0 + * @alias first + * @category Array + * @param {Array} array The array to query. + * @returns {*} Returns the first element of `array`. + * @example + * + * _.head([1, 2, 3]); + * // => 1 + * + * _.head([]); + * // => undefined + */ + function head(array) { + return (array && array.length) ? array[0] : undefined; + } + + /** + * Gets the index at which the first occurrence of `value` is found in `array` + * using [`SameValueZero`](http://ecma-international.org/ecma-262/7.0/#sec-samevaluezero) + * for equality comparisons. If `fromIndex` is negative, it's used as the + * offset from the end of `array`. + * + * @static + * @memberOf _ + * @since 0.1.0 + * @category Array + * @param {Array} array The array to inspect. + * @param {*} value The value to search for. + * @param {number} [fromIndex=0] The index to search from. + * @returns {number} Returns the index of the matched value, else `-1`. + * @example + * + * _.indexOf([1, 2, 1, 2], 2); + * // => 1 + * + * // Search from the `fromIndex`. + * _.indexOf([1, 2, 1, 2], 2, 2); + * // => 3 + */ + function indexOf(array, value, fromIndex) { + var length = array == null ? 0 : array.length; + if (!length) { + return -1; + } + var index = fromIndex == null ? 0 : toInteger(fromIndex); + if (index < 0) { + index = nativeMax(length + index, 0); + } + return baseIndexOf(array, value, index); + } + + /** + * Gets all but the last element of `array`. + * + * @static + * @memberOf _ + * @since 0.1.0 + * @category Array + * @param {Array} array The array to query. + * @returns {Array} Returns the slice of `array`. + * @example + * + * _.initial([1, 2, 3]); + * // => [1, 2] + */ + function initial(array) { + var length = array == null ? 0 : array.length; + return length ? baseSlice(array, 0, -1) : []; + } + + /** + * Creates an array of unique values that are included in all given arrays + * using [`SameValueZero`](http://ecma-international.org/ecma-262/7.0/#sec-samevaluezero) + * for equality comparisons. The order and references of result values are + * determined by the first array. + * + * @static + * @memberOf _ + * @since 0.1.0 + * @category Array + * @param {...Array} [arrays] The arrays to inspect. + * @returns {Array} Returns the new array of intersecting values. + * @example + * + * _.intersection([2, 1], [2, 3]); + * // => [2] + */ + var intersection = baseRest(function(arrays) { + var mapped = arrayMap(arrays, castArrayLikeObject); + return (mapped.length && mapped[0] === arrays[0]) + ? baseIntersection(mapped) + : []; + }); + + /** + * This method is like `_.intersection` except that it accepts `iteratee` + * which is invoked for each element of each `arrays` to generate the criterion + * by which they're compared. The order and references of result values are + * determined by the first array. The iteratee is invoked with one argument: + * (value). + * + * @static + * @memberOf _ + * @since 4.0.0 + * @category Array + * @param {...Array} [arrays] The arrays to inspect. + * @param {Function} [iteratee=_.identity] The iteratee invoked per element. + * @returns {Array} Returns the new array of intersecting values. + * @example + * + * _.intersectionBy([2.1, 1.2], [2.3, 3.4], Math.floor); + * // => [2.1] + * + * // The `_.property` iteratee shorthand. + * _.intersectionBy([{ 'x': 1 }], [{ 'x': 2 }, { 'x': 1 }], 'x'); + * // => [{ 'x': 1 }] + */ + var intersectionBy = baseRest(function(arrays) { + var iteratee = last(arrays), + mapped = arrayMap(arrays, castArrayLikeObject); + + if (iteratee === last(mapped)) { + iteratee = undefined; + } else { + mapped.pop(); + } + return (mapped.length && mapped[0] === arrays[0]) + ? baseIntersection(mapped, getIteratee(iteratee, 2)) + : []; + }); + + /** + * This method is like `_.intersection` except that it accepts `comparator` + * which is invoked to compare elements of `arrays`. The order and references + * of result values are determined by the first array. The comparator is + * invoked with two arguments: (arrVal, othVal). + * + * @static + * @memberOf _ + * @since 4.0.0 + * @category Array + * @param {...Array} [arrays] The arrays to inspect. + * @param {Function} [comparator] The comparator invoked per element. + * @returns {Array} Returns the new array of intersecting values. + * @example + * + * var objects = [{ 'x': 1, 'y': 2 }, { 'x': 2, 'y': 1 }]; + * var others = [{ 'x': 1, 'y': 1 }, { 'x': 1, 'y': 2 }]; + * + * _.intersectionWith(objects, others, _.isEqual); + * // => [{ 'x': 1, 'y': 2 }] + */ + var intersectionWith = baseRest(function(arrays) { + var comparator = last(arrays), + mapped = arrayMap(arrays, castArrayLikeObject); + + comparator = typeof comparator == 'function' ? comparator : undefined; + if (comparator) { + mapped.pop(); + } + return (mapped.length && mapped[0] === arrays[0]) + ? baseIntersection(mapped, undefined, comparator) + : []; + }); + + /** + * Converts all elements in `array` into a string separated by `separator`. + * + * @static + * @memberOf _ + * @since 4.0.0 + * @category Array + * @param {Array} array The array to convert. + * @param {string} [separator=','] The element separator. + * @returns {string} Returns the joined string. + * @example + * + * _.join(['a', 'b', 'c'], '~'); + * // => 'a~b~c' + */ + function join(array, separator) { + return array == null ? '' : nativeJoin.call(array, separator); + } + + /** + * Gets the last element of `array`. + * + * @static + * @memberOf _ + * @since 0.1.0 + * @category Array + * @param {Array} array The array to query. + * @returns {*} Returns the last element of `array`. + * @example + * + * _.last([1, 2, 3]); + * // => 3 + */ + function last(array) { + var length = array == null ? 0 : array.length; + return length ? array[length - 1] : undefined; + } + + /** + * This method is like `_.indexOf` except that it iterates over elements of + * `array` from right to left. + * + * @static + * @memberOf _ + * @since 0.1.0 + * @category Array + * @param {Array} array The array to inspect. + * @param {*} value The value to search for. + * @param {number} [fromIndex=array.length-1] The index to search from. + * @returns {number} Returns the index of the matched value, else `-1`. + * @example + * + * _.lastIndexOf([1, 2, 1, 2], 2); + * // => 3 + * + * // Search from the `fromIndex`. + * _.lastIndexOf([1, 2, 1, 2], 2, 2); + * // => 1 + */ + function lastIndexOf(array, value, fromIndex) { + var length = array == null ? 0 : array.length; + if (!length) { + return -1; + } + var index = length; + if (fromIndex !== undefined) { + index = toInteger(fromIndex); + index = index < 0 ? nativeMax(length + index, 0) : nativeMin(index, length - 1); + } + return value === value + ? strictLastIndexOf(array, value, index) + : baseFindIndex(array, baseIsNaN, index, true); + } + + /** + * Gets the element at index `n` of `array`. If `n` is negative, the nth + * element from the end is returned. + * + * @static + * @memberOf _ + * @since 4.11.0 + * @category Array + * @param {Array} array The array to query. + * @param {number} [n=0] The index of the element to return. + * @returns {*} Returns the nth element of `array`. + * @example + * + * var array = ['a', 'b', 'c', 'd']; + * + * _.nth(array, 1); + * // => 'b' + * + * _.nth(array, -2); + * // => 'c'; + */ + function nth(array, n) { + return (array && array.length) ? baseNth(array, toInteger(n)) : undefined; + } + + /** + * Removes all given values from `array` using + * [`SameValueZero`](http://ecma-international.org/ecma-262/7.0/#sec-samevaluezero) + * for equality comparisons. + * + * **Note:** Unlike `_.without`, this method mutates `array`. Use `_.remove` + * to remove elements from an array by predicate. + * + * @static + * @memberOf _ + * @since 2.0.0 + * @category Array + * @param {Array} array The array to modify. + * @param {...*} [values] The values to remove. + * @returns {Array} Returns `array`. + * @example + * + * var array = ['a', 'b', 'c', 'a', 'b', 'c']; + * + * _.pull(array, 'a', 'c'); + * console.log(array); + * // => ['b', 'b'] + */ + var pull = baseRest(pullAll); + + /** + * This method is like `_.pull` except that it accepts an array of values to remove. + * + * **Note:** Unlike `_.difference`, this method mutates `array`. + * + * @static + * @memberOf _ + * @since 4.0.0 + * @category Array + * @param {Array} array The array to modify. + * @param {Array} values The values to remove. + * @returns {Array} Returns `array`. + * @example + * + * var array = ['a', 'b', 'c', 'a', 'b', 'c']; + * + * _.pullAll(array, ['a', 'c']); + * console.log(array); + * // => ['b', 'b'] + */ + function pullAll(array, values) { + return (array && array.length && values && values.length) + ? basePullAll(array, values) + : array; + } + + /** + * This method is like `_.pullAll` except that it accepts `iteratee` which is + * invoked for each element of `array` and `values` to generate the criterion + * by which they're compared. The iteratee is invoked with one argument: (value). + * + * **Note:** Unlike `_.differenceBy`, this method mutates `array`. + * + * @static + * @memberOf _ + * @since 4.0.0 + * @category Array + * @param {Array} array The array to modify. + * @param {Array} values The values to remove. + * @param {Function} [iteratee=_.identity] The iteratee invoked per element. + * @returns {Array} Returns `array`. + * @example + * + * var array = [{ 'x': 1 }, { 'x': 2 }, { 'x': 3 }, { 'x': 1 }]; + * + * _.pullAllBy(array, [{ 'x': 1 }, { 'x': 3 }], 'x'); + * console.log(array); + * // => [{ 'x': 2 }] + */ + function pullAllBy(array, values, iteratee) { + return (array && array.length && values && values.length) + ? basePullAll(array, values, getIteratee(iteratee, 2)) + : array; + } + + /** + * This method is like `_.pullAll` except that it accepts `comparator` which + * is invoked to compare elements of `array` to `values`. The comparator is + * invoked with two arguments: (arrVal, othVal). + * + * **Note:** Unlike `_.differenceWith`, this method mutates `array`. + * + * @static + * @memberOf _ + * @since 4.6.0 + * @category Array + * @param {Array} array The array to modify. + * @param {Array} values The values to remove. + * @param {Function} [comparator] The comparator invoked per element. + * @returns {Array} Returns `array`. + * @example + * + * var array = [{ 'x': 1, 'y': 2 }, { 'x': 3, 'y': 4 }, { 'x': 5, 'y': 6 }]; + * + * _.pullAllWith(array, [{ 'x': 3, 'y': 4 }], _.isEqual); + * console.log(array); + * // => [{ 'x': 1, 'y': 2 }, { 'x': 5, 'y': 6 }] + */ + function pullAllWith(array, values, comparator) { + return (array && array.length && values && values.length) + ? basePullAll(array, values, undefined, comparator) + : array; + } + + /** + * Removes elements from `array` corresponding to `indexes` and returns an + * array of removed elements. + * + * **Note:** Unlike `_.at`, this method mutates `array`. + * + * @static + * @memberOf _ + * @since 3.0.0 + * @category Array + * @param {Array} array The array to modify. + * @param {...(number|number[])} [indexes] The indexes of elements to remove. + * @returns {Array} Returns the new array of removed elements. + * @example + * + * var array = ['a', 'b', 'c', 'd']; + * var pulled = _.pullAt(array, [1, 3]); + * + * console.log(array); + * // => ['a', 'c'] + * + * console.log(pulled); + * // => ['b', 'd'] + */ + var pullAt = flatRest(function(array, indexes) { + var length = array == null ? 0 : array.length, + result = baseAt(array, indexes); + + basePullAt(array, arrayMap(indexes, function(index) { + return isIndex(index, length) ? +index : index; + }).sort(compareAscending)); + + return result; + }); + + /** + * Removes all elements from `array` that `predicate` returns truthy for + * and returns an array of the removed elements. The predicate is invoked + * with three arguments: (value, index, array). + * + * **Note:** Unlike `_.filter`, this method mutates `array`. Use `_.pull` + * to pull elements from an array by value. + * + * @static + * @memberOf _ + * @since 2.0.0 + * @category Array + * @param {Array} array The array to modify. + * @param {Function} [predicate=_.identity] The function invoked per iteration. + * @returns {Array} Returns the new array of removed elements. + * @example + * + * var array = [1, 2, 3, 4]; + * var evens = _.remove(array, function(n) { + * return n % 2 == 0; + * }); + * + * console.log(array); + * // => [1, 3] + * + * console.log(evens); + * // => [2, 4] + */ + function remove(array, predicate) { + var result = []; + if (!(array && array.length)) { + return result; + } + var index = -1, + indexes = [], + length = array.length; + + predicate = getIteratee(predicate, 3); + while (++index < length) { + var value = array[index]; + if (predicate(value, index, array)) { + result.push(value); + indexes.push(index); + } + } + basePullAt(array, indexes); + return result; + } + + /** + * Reverses `array` so that the first element becomes the last, the second + * element becomes the second to last, and so on. + * + * **Note:** This method mutates `array` and is based on + * [`Array#reverse`](https://mdn.io/Array/reverse). + * + * @static + * @memberOf _ + * @since 4.0.0 + * @category Array + * @param {Array} array The array to modify. + * @returns {Array} Returns `array`. + * @example + * + * var array = [1, 2, 3]; + * + * _.reverse(array); + * // => [3, 2, 1] + * + * console.log(array); + * // => [3, 2, 1] + */ + function reverse(array) { + return array == null ? array : nativeReverse.call(array); + } + + /** + * Creates a slice of `array` from `start` up to, but not including, `end`. + * + * **Note:** This method is used instead of + * [`Array#slice`](https://mdn.io/Array/slice) to ensure dense arrays are + * returned. + * + * @static + * @memberOf _ + * @since 3.0.0 + * @category Array + * @param {Array} array The array to slice. + * @param {number} [start=0] The start position. + * @param {number} [end=array.length] The end position. + * @returns {Array} Returns the slice of `array`. + */ + function slice(array, start, end) { + var length = array == null ? 0 : array.length; + if (!length) { + return []; + } + if (end && typeof end != 'number' && isIterateeCall(array, start, end)) { + start = 0; + end = length; + } + else { + start = start == null ? 0 : toInteger(start); + end = end === undefined ? length : toInteger(end); + } + return baseSlice(array, start, end); + } + + /** + * Uses a binary search to determine the lowest index at which `value` + * should be inserted into `array` in order to maintain its sort order. + * + * @static + * @memberOf _ + * @since 0.1.0 + * @category Array + * @param {Array} array The sorted array to inspect. + * @param {*} value The value to evaluate. + * @returns {number} Returns the index at which `value` should be inserted + * into `array`. + * @example + * + * _.sortedIndex([30, 50], 40); + * // => 1 + */ + function sortedIndex(array, value) { + return baseSortedIndex(array, value); + } + + /** + * This method is like `_.sortedIndex` except that it accepts `iteratee` + * which is invoked for `value` and each element of `array` to compute their + * sort ranking. The iteratee is invoked with one argument: (value). + * + * @static + * @memberOf _ + * @since 4.0.0 + * @category Array + * @param {Array} array The sorted array to inspect. + * @param {*} value The value to evaluate. + * @param {Function} [iteratee=_.identity] The iteratee invoked per element. + * @returns {number} Returns the index at which `value` should be inserted + * into `array`. + * @example + * + * var objects = [{ 'x': 4 }, { 'x': 5 }]; + * + * _.sortedIndexBy(objects, { 'x': 4 }, function(o) { return o.x; }); + * // => 0 + * + * // The `_.property` iteratee shorthand. + * _.sortedIndexBy(objects, { 'x': 4 }, 'x'); + * // => 0 + */ + function sortedIndexBy(array, value, iteratee) { + return baseSortedIndexBy(array, value, getIteratee(iteratee, 2)); + } + + /** + * This method is like `_.indexOf` except that it performs a binary + * search on a sorted `array`. + * + * @static + * @memberOf _ + * @since 4.0.0 + * @category Array + * @param {Array} array The array to inspect. + * @param {*} value The value to search for. + * @returns {number} Returns the index of the matched value, else `-1`. + * @example + * + * _.sortedIndexOf([4, 5, 5, 5, 6], 5); + * // => 1 + */ + function sortedIndexOf(array, value) { + var length = array == null ? 0 : array.length; + if (length) { + var index = baseSortedIndex(array, value); + if (index < length && eq(array[index], value)) { + return index; + } + } + return -1; + } + + /** + * This method is like `_.sortedIndex` except that it returns the highest + * index at which `value` should be inserted into `array` in order to + * maintain its sort order. + * + * @static + * @memberOf _ + * @since 3.0.0 + * @category Array + * @param {Array} array The sorted array to inspect. + * @param {*} value The value to evaluate. + * @returns {number} Returns the index at which `value` should be inserted + * into `array`. + * @example + * + * _.sortedLastIndex([4, 5, 5, 5, 6], 5); + * // => 4 + */ + function sortedLastIndex(array, value) { + return baseSortedIndex(array, value, true); + } + + /** + * This method is like `_.sortedLastIndex` except that it accepts `iteratee` + * which is invoked for `value` and each element of `array` to compute their + * sort ranking. The iteratee is invoked with one argument: (value). + * + * @static + * @memberOf _ + * @since 4.0.0 + * @category Array + * @param {Array} array The sorted array to inspect. + * @param {*} value The value to evaluate. + * @param {Function} [iteratee=_.identity] The iteratee invoked per element. + * @returns {number} Returns the index at which `value` should be inserted + * into `array`. + * @example + * + * var objects = [{ 'x': 4 }, { 'x': 5 }]; + * + * _.sortedLastIndexBy(objects, { 'x': 4 }, function(o) { return o.x; }); + * // => 1 + * + * // The `_.property` iteratee shorthand. + * _.sortedLastIndexBy(objects, { 'x': 4 }, 'x'); + * // => 1 + */ + function sortedLastIndexBy(array, value, iteratee) { + return baseSortedIndexBy(array, value, getIteratee(iteratee, 2), true); + } + + /** + * This method is like `_.lastIndexOf` except that it performs a binary + * search on a sorted `array`. + * + * @static + * @memberOf _ + * @since 4.0.0 + * @category Array + * @param {Array} array The array to inspect. + * @param {*} value The value to search for. + * @returns {number} Returns the index of the matched value, else `-1`. + * @example + * + * _.sortedLastIndexOf([4, 5, 5, 5, 6], 5); + * // => 3 + */ + function sortedLastIndexOf(array, value) { + var length = array == null ? 0 : array.length; + if (length) { + var index = baseSortedIndex(array, value, true) - 1; + if (eq(array[index], value)) { + return index; + } + } + return -1; + } + + /** + * This method is like `_.uniq` except that it's designed and optimized + * for sorted arrays. + * + * @static + * @memberOf _ + * @since 4.0.0 + * @category Array + * @param {Array} array The array to inspect. + * @returns {Array} Returns the new duplicate free array. + * @example + * + * _.sortedUniq([1, 1, 2]); + * // => [1, 2] + */ + function sortedUniq(array) { + return (array && array.length) + ? baseSortedUniq(array) + : []; + } + + /** + * This method is like `_.uniqBy` except that it's designed and optimized + * for sorted arrays. + * + * @static + * @memberOf _ + * @since 4.0.0 + * @category Array + * @param {Array} array The array to inspect. + * @param {Function} [iteratee] The iteratee invoked per element. + * @returns {Array} Returns the new duplicate free array. + * @example + * + * _.sortedUniqBy([1.1, 1.2, 2.3, 2.4], Math.floor); + * // => [1.1, 2.3] + */ + function sortedUniqBy(array, iteratee) { + return (array && array.length) + ? baseSortedUniq(array, getIteratee(iteratee, 2)) + : []; + } + + /** + * Gets all but the first element of `array`. + * + * @static + * @memberOf _ + * @since 4.0.0 + * @category Array + * @param {Array} array The array to query. + * @returns {Array} Returns the slice of `array`. + * @example + * + * _.tail([1, 2, 3]); + * // => [2, 3] + */ + function tail(array) { + var length = array == null ? 0 : array.length; + return length ? baseSlice(array, 1, length) : []; + } + + /** + * Creates a slice of `array` with `n` elements taken from the beginning. + * + * @static + * @memberOf _ + * @since 0.1.0 + * @category Array + * @param {Array} array The array to query. + * @param {number} [n=1] The number of elements to take. + * @param- {Object} [guard] Enables use as an iteratee for methods like `_.map`. + * @returns {Array} Returns the slice of `array`. + * @example + * + * _.take([1, 2, 3]); + * // => [1] + * + * _.take([1, 2, 3], 2); + * // => [1, 2] + * + * _.take([1, 2, 3], 5); + * // => [1, 2, 3] + * + * _.take([1, 2, 3], 0); + * // => [] + */ + function take(array, n, guard) { + if (!(array && array.length)) { + return []; + } + n = (guard || n === undefined) ? 1 : toInteger(n); + return baseSlice(array, 0, n < 0 ? 0 : n); + } + + /** + * Creates a slice of `array` with `n` elements taken from the end. + * + * @static + * @memberOf _ + * @since 3.0.0 + * @category Array + * @param {Array} array The array to query. + * @param {number} [n=1] The number of elements to take. + * @param- {Object} [guard] Enables use as an iteratee for methods like `_.map`. + * @returns {Array} Returns the slice of `array`. + * @example + * + * _.takeRight([1, 2, 3]); + * // => [3] + * + * _.takeRight([1, 2, 3], 2); + * // => [2, 3] + * + * _.takeRight([1, 2, 3], 5); + * // => [1, 2, 3] + * + * _.takeRight([1, 2, 3], 0); + * // => [] + */ + function takeRight(array, n, guard) { + var length = array == null ? 0 : array.length; + if (!length) { + return []; + } + n = (guard || n === undefined) ? 1 : toInteger(n); + n = length - n; + return baseSlice(array, n < 0 ? 0 : n, length); + } + + /** + * Creates a slice of `array` with elements taken from the end. Elements are + * taken until `predicate` returns falsey. The predicate is invoked with + * three arguments: (value, index, array). + * + * @static + * @memberOf _ + * @since 3.0.0 + * @category Array + * @param {Array} array The array to query. + * @param {Function} [predicate=_.identity] The function invoked per iteration. + * @returns {Array} Returns the slice of `array`. + * @example + * + * var users = [ + * { 'user': 'barney', 'active': true }, + * { 'user': 'fred', 'active': false }, + * { 'user': 'pebbles', 'active': false } + * ]; + * + * _.takeRightWhile(users, function(o) { return !o.active; }); + * // => objects for ['fred', 'pebbles'] + * + * // The `_.matches` iteratee shorthand. + * _.takeRightWhile(users, { 'user': 'pebbles', 'active': false }); + * // => objects for ['pebbles'] + * + * // The `_.matchesProperty` iteratee shorthand. + * _.takeRightWhile(users, ['active', false]); + * // => objects for ['fred', 'pebbles'] + * + * // The `_.property` iteratee shorthand. + * _.takeRightWhile(users, 'active'); + * // => [] + */ + function takeRightWhile(array, predicate) { + return (array && array.length) + ? baseWhile(array, getIteratee(predicate, 3), false, true) + : []; + } + + /** + * Creates a slice of `array` with elements taken from the beginning. Elements + * are taken until `predicate` returns falsey. The predicate is invoked with + * three arguments: (value, index, array). + * + * @static + * @memberOf _ + * @since 3.0.0 + * @category Array + * @param {Array} array The array to query. + * @param {Function} [predicate=_.identity] The function invoked per iteration. + * @returns {Array} Returns the slice of `array`. + * @example + * + * var users = [ + * { 'user': 'barney', 'active': false }, + * { 'user': 'fred', 'active': false }, + * { 'user': 'pebbles', 'active': true } + * ]; + * + * _.takeWhile(users, function(o) { return !o.active; }); + * // => objects for ['barney', 'fred'] + * + * // The `_.matches` iteratee shorthand. + * _.takeWhile(users, { 'user': 'barney', 'active': false }); + * // => objects for ['barney'] + * + * // The `_.matchesProperty` iteratee shorthand. + * _.takeWhile(users, ['active', false]); + * // => objects for ['barney', 'fred'] + * + * // The `_.property` iteratee shorthand. + * _.takeWhile(users, 'active'); + * // => [] + */ + function takeWhile(array, predicate) { + return (array && array.length) + ? baseWhile(array, getIteratee(predicate, 3)) + : []; + } + + /** + * Creates an array of unique values, in order, from all given arrays using + * [`SameValueZero`](http://ecma-international.org/ecma-262/7.0/#sec-samevaluezero) + * for equality comparisons. + * + * @static + * @memberOf _ + * @since 0.1.0 + * @category Array + * @param {...Array} [arrays] The arrays to inspect. + * @returns {Array} Returns the new array of combined values. + * @example + * + * _.union([2], [1, 2]); + * // => [2, 1] + */ + var union = baseRest(function(arrays) { + return baseUniq(baseFlatten(arrays, 1, isArrayLikeObject, true)); + }); + + /** + * This method is like `_.union` except that it accepts `iteratee` which is + * invoked for each element of each `arrays` to generate the criterion by + * which uniqueness is computed. Result values are chosen from the first + * array in which the value occurs. The iteratee is invoked with one argument: + * (value). + * + * @static + * @memberOf _ + * @since 4.0.0 + * @category Array + * @param {...Array} [arrays] The arrays to inspect. + * @param {Function} [iteratee=_.identity] The iteratee invoked per element. + * @returns {Array} Returns the new array of combined values. + * @example + * + * _.unionBy([2.1], [1.2, 2.3], Math.floor); + * // => [2.1, 1.2] + * + * // The `_.property` iteratee shorthand. + * _.unionBy([{ 'x': 1 }], [{ 'x': 2 }, { 'x': 1 }], 'x'); + * // => [{ 'x': 1 }, { 'x': 2 }] + */ + var unionBy = baseRest(function(arrays) { + var iteratee = last(arrays); + if (isArrayLikeObject(iteratee)) { + iteratee = undefined; + } + return baseUniq(baseFlatten(arrays, 1, isArrayLikeObject, true), getIteratee(iteratee, 2)); + }); + + /** + * This method is like `_.union` except that it accepts `comparator` which + * is invoked to compare elements of `arrays`. Result values are chosen from + * the first array in which the value occurs. The comparator is invoked + * with two arguments: (arrVal, othVal). + * + * @static + * @memberOf _ + * @since 4.0.0 + * @category Array + * @param {...Array} [arrays] The arrays to inspect. + * @param {Function} [comparator] The comparator invoked per element. + * @returns {Array} Returns the new array of combined values. + * @example + * + * var objects = [{ 'x': 1, 'y': 2 }, { 'x': 2, 'y': 1 }]; + * var others = [{ 'x': 1, 'y': 1 }, { 'x': 1, 'y': 2 }]; + * + * _.unionWith(objects, others, _.isEqual); + * // => [{ 'x': 1, 'y': 2 }, { 'x': 2, 'y': 1 }, { 'x': 1, 'y': 1 }] + */ + var unionWith = baseRest(function(arrays) { + var comparator = last(arrays); + comparator = typeof comparator == 'function' ? comparator : undefined; + return baseUniq(baseFlatten(arrays, 1, isArrayLikeObject, true), undefined, comparator); + }); + + /** + * Creates a duplicate-free version of an array, using + * [`SameValueZero`](http://ecma-international.org/ecma-262/7.0/#sec-samevaluezero) + * for equality comparisons, in which only the first occurrence of each element + * is kept. The order of result values is determined by the order they occur + * in the array. + * + * @static + * @memberOf _ + * @since 0.1.0 + * @category Array + * @param {Array} array The array to inspect. + * @returns {Array} Returns the new duplicate free array. + * @example + * + * _.uniq([2, 1, 2]); + * // => [2, 1] + */ + function uniq(array) { + return (array && array.length) ? baseUniq(array) : []; + } + + /** + * This method is like `_.uniq` except that it accepts `iteratee` which is + * invoked for each element in `array` to generate the criterion by which + * uniqueness is computed. The order of result values is determined by the + * order they occur in the array. The iteratee is invoked with one argument: + * (value). + * + * @static + * @memberOf _ + * @since 4.0.0 + * @category Array + * @param {Array} array The array to inspect. + * @param {Function} [iteratee=_.identity] The iteratee invoked per element. + * @returns {Array} Returns the new duplicate free array. + * @example + * + * _.uniqBy([2.1, 1.2, 2.3], Math.floor); + * // => [2.1, 1.2] + * + * // The `_.property` iteratee shorthand. + * _.uniqBy([{ 'x': 1 }, { 'x': 2 }, { 'x': 1 }], 'x'); + * // => [{ 'x': 1 }, { 'x': 2 }] + */ + function uniqBy(array, iteratee) { + return (array && array.length) ? baseUniq(array, getIteratee(iteratee, 2)) : []; + } + + /** + * This method is like `_.uniq` except that it accepts `comparator` which + * is invoked to compare elements of `array`. The order of result values is + * determined by the order they occur in the array.The comparator is invoked + * with two arguments: (arrVal, othVal). + * + * @static + * @memberOf _ + * @since 4.0.0 + * @category Array + * @param {Array} array The array to inspect. + * @param {Function} [comparator] The comparator invoked per element. + * @returns {Array} Returns the new duplicate free array. + * @example + * + * var objects = [{ 'x': 1, 'y': 2 }, { 'x': 2, 'y': 1 }, { 'x': 1, 'y': 2 }]; + * + * _.uniqWith(objects, _.isEqual); + * // => [{ 'x': 1, 'y': 2 }, { 'x': 2, 'y': 1 }] + */ + function uniqWith(array, comparator) { + comparator = typeof comparator == 'function' ? comparator : undefined; + return (array && array.length) ? baseUniq(array, undefined, comparator) : []; + } + + /** + * This method is like `_.zip` except that it accepts an array of grouped + * elements and creates an array regrouping the elements to their pre-zip + * configuration. + * + * @static + * @memberOf _ + * @since 1.2.0 + * @category Array + * @param {Array} array The array of grouped elements to process. + * @returns {Array} Returns the new array of regrouped elements. + * @example + * + * var zipped = _.zip(['a', 'b'], [1, 2], [true, false]); + * // => [['a', 1, true], ['b', 2, false]] + * + * _.unzip(zipped); + * // => [['a', 'b'], [1, 2], [true, false]] + */ + function unzip(array) { + if (!(array && array.length)) { + return []; + } + var length = 0; + array = arrayFilter(array, function(group) { + if (isArrayLikeObject(group)) { + length = nativeMax(group.length, length); + return true; + } + }); + return baseTimes(length, function(index) { + return arrayMap(array, baseProperty(index)); + }); + } + + /** + * This method is like `_.unzip` except that it accepts `iteratee` to specify + * how regrouped values should be combined. The iteratee is invoked with the + * elements of each group: (...group). + * + * @static + * @memberOf _ + * @since 3.8.0 + * @category Array + * @param {Array} array The array of grouped elements to process. + * @param {Function} [iteratee=_.identity] The function to combine + * regrouped values. + * @returns {Array} Returns the new array of regrouped elements. + * @example + * + * var zipped = _.zip([1, 2], [10, 20], [100, 200]); + * // => [[1, 10, 100], [2, 20, 200]] + * + * _.unzipWith(zipped, _.add); + * // => [3, 30, 300] + */ + function unzipWith(array, iteratee) { + if (!(array && array.length)) { + return []; + } + var result = unzip(array); + if (iteratee == null) { + return result; + } + return arrayMap(result, function(group) { + return apply(iteratee, undefined, group); + }); + } + + /** + * Creates an array excluding all given values using + * [`SameValueZero`](http://ecma-international.org/ecma-262/7.0/#sec-samevaluezero) + * for equality comparisons. + * + * **Note:** Unlike `_.pull`, this method returns a new array. + * + * @static + * @memberOf _ + * @since 0.1.0 + * @category Array + * @param {Array} array The array to inspect. + * @param {...*} [values] The values to exclude. + * @returns {Array} Returns the new array of filtered values. + * @see _.difference, _.xor + * @example + * + * _.without([2, 1, 2, 3], 1, 2); + * // => [3] + */ + var without = baseRest(function(array, values) { + return isArrayLikeObject(array) + ? baseDifference(array, values) + : []; + }); + + /** + * Creates an array of unique values that is the + * [symmetric difference](https://en.wikipedia.org/wiki/Symmetric_difference) + * of the given arrays. The order of result values is determined by the order + * they occur in the arrays. + * + * @static + * @memberOf _ + * @since 2.4.0 + * @category Array + * @param {...Array} [arrays] The arrays to inspect. + * @returns {Array} Returns the new array of filtered values. + * @see _.difference, _.without + * @example + * + * _.xor([2, 1], [2, 3]); + * // => [1, 3] + */ + var xor = baseRest(function(arrays) { + return baseXor(arrayFilter(arrays, isArrayLikeObject)); + }); + + /** + * This method is like `_.xor` except that it accepts `iteratee` which is + * invoked for each element of each `arrays` to generate the criterion by + * which by which they're compared. The order of result values is determined + * by the order they occur in the arrays. The iteratee is invoked with one + * argument: (value). + * + * @static + * @memberOf _ + * @since 4.0.0 + * @category Array + * @param {...Array} [arrays] The arrays to inspect. + * @param {Function} [iteratee=_.identity] The iteratee invoked per element. + * @returns {Array} Returns the new array of filtered values. + * @example + * + * _.xorBy([2.1, 1.2], [2.3, 3.4], Math.floor); + * // => [1.2, 3.4] + * + * // The `_.property` iteratee shorthand. + * _.xorBy([{ 'x': 1 }], [{ 'x': 2 }, { 'x': 1 }], 'x'); + * // => [{ 'x': 2 }] + */ + var xorBy = baseRest(function(arrays) { + var iteratee = last(arrays); + if (isArrayLikeObject(iteratee)) { + iteratee = undefined; + } + return baseXor(arrayFilter(arrays, isArrayLikeObject), getIteratee(iteratee, 2)); + }); + + /** + * This method is like `_.xor` except that it accepts `comparator` which is + * invoked to compare elements of `arrays`. The order of result values is + * determined by the order they occur in the arrays. The comparator is invoked + * with two arguments: (arrVal, othVal). + * + * @static + * @memberOf _ + * @since 4.0.0 + * @category Array + * @param {...Array} [arrays] The arrays to inspect. + * @param {Function} [comparator] The comparator invoked per element. + * @returns {Array} Returns the new array of filtered values. + * @example + * + * var objects = [{ 'x': 1, 'y': 2 }, { 'x': 2, 'y': 1 }]; + * var others = [{ 'x': 1, 'y': 1 }, { 'x': 1, 'y': 2 }]; + * + * _.xorWith(objects, others, _.isEqual); + * // => [{ 'x': 2, 'y': 1 }, { 'x': 1, 'y': 1 }] + */ + var xorWith = baseRest(function(arrays) { + var comparator = last(arrays); + comparator = typeof comparator == 'function' ? comparator : undefined; + return baseXor(arrayFilter(arrays, isArrayLikeObject), undefined, comparator); + }); + + /** + * Creates an array of grouped elements, the first of which contains the + * first elements of the given arrays, the second of which contains the + * second elements of the given arrays, and so on. + * + * @static + * @memberOf _ + * @since 0.1.0 + * @category Array + * @param {...Array} [arrays] The arrays to process. + * @returns {Array} Returns the new array of grouped elements. + * @example + * + * _.zip(['a', 'b'], [1, 2], [true, false]); + * // => [['a', 1, true], ['b', 2, false]] + */ + var zip = baseRest(unzip); + + /** + * This method is like `_.fromPairs` except that it accepts two arrays, + * one of property identifiers and one of corresponding values. + * + * @static + * @memberOf _ + * @since 0.4.0 + * @category Array + * @param {Array} [props=[]] The property identifiers. + * @param {Array} [values=[]] The property values. + * @returns {Object} Returns the new object. + * @example + * + * _.zipObject(['a', 'b'], [1, 2]); + * // => { 'a': 1, 'b': 2 } + */ + function zipObject(props, values) { + return baseZipObject(props || [], values || [], assignValue); + } + + /** + * This method is like `_.zipObject` except that it supports property paths. + * + * @static + * @memberOf _ + * @since 4.1.0 + * @category Array + * @param {Array} [props=[]] The property identifiers. + * @param {Array} [values=[]] The property values. + * @returns {Object} Returns the new object. + * @example + * + * _.zipObjectDeep(['a.b[0].c', 'a.b[1].d'], [1, 2]); + * // => { 'a': { 'b': [{ 'c': 1 }, { 'd': 2 }] } } + */ + function zipObjectDeep(props, values) { + return baseZipObject(props || [], values || [], baseSet); + } + + /** + * This method is like `_.zip` except that it accepts `iteratee` to specify + * how grouped values should be combined. The iteratee is invoked with the + * elements of each group: (...group). + * + * @static + * @memberOf _ + * @since 3.8.0 + * @category Array + * @param {...Array} [arrays] The arrays to process. + * @param {Function} [iteratee=_.identity] The function to combine + * grouped values. + * @returns {Array} Returns the new array of grouped elements. + * @example + * + * _.zipWith([1, 2], [10, 20], [100, 200], function(a, b, c) { + * return a + b + c; + * }); + * // => [111, 222] + */ + var zipWith = baseRest(function(arrays) { + var length = arrays.length, + iteratee = length > 1 ? arrays[length - 1] : undefined; + + iteratee = typeof iteratee == 'function' ? (arrays.pop(), iteratee) : undefined; + return unzipWith(arrays, iteratee); + }); + + /*------------------------------------------------------------------------*/ + + /** + * Creates a `lodash` wrapper instance that wraps `value` with explicit method + * chain sequences enabled. The result of such sequences must be unwrapped + * with `_#value`. + * + * @static + * @memberOf _ + * @since 1.3.0 + * @category Seq + * @param {*} value The value to wrap. + * @returns {Object} Returns the new `lodash` wrapper instance. + * @example + * + * var users = [ + * { 'user': 'barney', 'age': 36 }, + * { 'user': 'fred', 'age': 40 }, + * { 'user': 'pebbles', 'age': 1 } + * ]; + * + * var youngest = _ + * .chain(users) + * .sortBy('age') + * .map(function(o) { + * return o.user + ' is ' + o.age; + * }) + * .head() + * .value(); + * // => 'pebbles is 1' + */ + function chain(value) { + var result = lodash(value); + result.__chain__ = true; + return result; + } + + /** + * This method invokes `interceptor` and returns `value`. The interceptor + * is invoked with one argument; (value). The purpose of this method is to + * "tap into" a method chain sequence in order to modify intermediate results. + * + * @static + * @memberOf _ + * @since 0.1.0 + * @category Seq + * @param {*} value The value to provide to `interceptor`. + * @param {Function} interceptor The function to invoke. + * @returns {*} Returns `value`. + * @example + * + * _([1, 2, 3]) + * .tap(function(array) { + * // Mutate input array. + * array.pop(); + * }) + * .reverse() + * .value(); + * // => [2, 1] + */ + function tap(value, interceptor) { + interceptor(value); + return value; + } + + /** + * This method is like `_.tap` except that it returns the result of `interceptor`. + * The purpose of this method is to "pass thru" values replacing intermediate + * results in a method chain sequence. + * + * @static + * @memberOf _ + * @since 3.0.0 + * @category Seq + * @param {*} value The value to provide to `interceptor`. + * @param {Function} interceptor The function to invoke. + * @returns {*} Returns the result of `interceptor`. + * @example + * + * _(' abc ') + * .chain() + * .trim() + * .thru(function(value) { + * return [value]; + * }) + * .value(); + * // => ['abc'] + */ + function thru(value, interceptor) { + return interceptor(value); + } + + /** + * This method is the wrapper version of `_.at`. + * + * @name at + * @memberOf _ + * @since 1.0.0 + * @category Seq + * @param {...(string|string[])} [paths] The property paths to pick. + * @returns {Object} Returns the new `lodash` wrapper instance. + * @example + * + * var object = { 'a': [{ 'b': { 'c': 3 } }, 4] }; + * + * _(object).at(['a[0].b.c', 'a[1]']).value(); + * // => [3, 4] + */ + var wrapperAt = flatRest(function(paths) { + var length = paths.length, + start = length ? paths[0] : 0, + value = this.__wrapped__, + interceptor = function(object) { return baseAt(object, paths); }; + + if (length > 1 || this.__actions__.length || + !(value instanceof LazyWrapper) || !isIndex(start)) { + return this.thru(interceptor); + } + value = value.slice(start, +start + (length ? 1 : 0)); + value.__actions__.push({ + 'func': thru, + 'args': [interceptor], + 'thisArg': undefined + }); + return new LodashWrapper(value, this.__chain__).thru(function(array) { + if (length && !array.length) { + array.push(undefined); + } + return array; + }); + }); + + /** + * Creates a `lodash` wrapper instance with explicit method chain sequences enabled. + * + * @name chain + * @memberOf _ + * @since 0.1.0 + * @category Seq + * @returns {Object} Returns the new `lodash` wrapper instance. + * @example + * + * var users = [ + * { 'user': 'barney', 'age': 36 }, + * { 'user': 'fred', 'age': 40 } + * ]; + * + * // A sequence without explicit chaining. + * _(users).head(); + * // => { 'user': 'barney', 'age': 36 } + * + * // A sequence with explicit chaining. + * _(users) + * .chain() + * .head() + * .pick('user') + * .value(); + * // => { 'user': 'barney' } + */ + function wrapperChain() { + return chain(this); + } + + /** + * Executes the chain sequence and returns the wrapped result. + * + * @name commit + * @memberOf _ + * @since 3.2.0 + * @category Seq + * @returns {Object} Returns the new `lodash` wrapper instance. + * @example + * + * var array = [1, 2]; + * var wrapped = _(array).push(3); + * + * console.log(array); + * // => [1, 2] + * + * wrapped = wrapped.commit(); + * console.log(array); + * // => [1, 2, 3] + * + * wrapped.last(); + * // => 3 + * + * console.log(array); + * // => [1, 2, 3] + */ + function wrapperCommit() { + return new LodashWrapper(this.value(), this.__chain__); + } + + /** + * Gets the next value on a wrapped object following the + * [iterator protocol](https://mdn.io/iteration_protocols#iterator). + * + * @name next + * @memberOf _ + * @since 4.0.0 + * @category Seq + * @returns {Object} Returns the next iterator value. + * @example + * + * var wrapped = _([1, 2]); + * + * wrapped.next(); + * // => { 'done': false, 'value': 1 } + * + * wrapped.next(); + * // => { 'done': false, 'value': 2 } + * + * wrapped.next(); + * // => { 'done': true, 'value': undefined } + */ + function wrapperNext() { + if (this.__values__ === undefined) { + this.__values__ = toArray(this.value()); + } + var done = this.__index__ >= this.__values__.length, + value = done ? undefined : this.__values__[this.__index__++]; + + return { 'done': done, 'value': value }; + } + + /** + * Enables the wrapper to be iterable. + * + * @name Symbol.iterator + * @memberOf _ + * @since 4.0.0 + * @category Seq + * @returns {Object} Returns the wrapper object. + * @example + * + * var wrapped = _([1, 2]); + * + * wrapped[Symbol.iterator]() === wrapped; + * // => true + * + * Array.from(wrapped); + * // => [1, 2] + */ + function wrapperToIterator() { + return this; + } + + /** + * Creates a clone of the chain sequence planting `value` as the wrapped value. + * + * @name plant + * @memberOf _ + * @since 3.2.0 + * @category Seq + * @param {*} value The value to plant. + * @returns {Object} Returns the new `lodash` wrapper instance. + * @example + * + * function square(n) { + * return n * n; + * } + * + * var wrapped = _([1, 2]).map(square); + * var other = wrapped.plant([3, 4]); + * + * other.value(); + * // => [9, 16] + * + * wrapped.value(); + * // => [1, 4] + */ + function wrapperPlant(value) { + var result, + parent = this; + + while (parent instanceof baseLodash) { + var clone = wrapperClone(parent); + clone.__index__ = 0; + clone.__values__ = undefined; + if (result) { + previous.__wrapped__ = clone; + } else { + result = clone; + } + var previous = clone; + parent = parent.__wrapped__; + } + previous.__wrapped__ = value; + return result; + } + + /** + * This method is the wrapper version of `_.reverse`. + * + * **Note:** This method mutates the wrapped array. + * + * @name reverse + * @memberOf _ + * @since 0.1.0 + * @category Seq + * @returns {Object} Returns the new `lodash` wrapper instance. + * @example + * + * var array = [1, 2, 3]; + * + * _(array).reverse().value() + * // => [3, 2, 1] + * + * console.log(array); + * // => [3, 2, 1] + */ + function wrapperReverse() { + var value = this.__wrapped__; + if (value instanceof LazyWrapper) { + var wrapped = value; + if (this.__actions__.length) { + wrapped = new LazyWrapper(this); + } + wrapped = wrapped.reverse(); + wrapped.__actions__.push({ + 'func': thru, + 'args': [reverse], + 'thisArg': undefined + }); + return new LodashWrapper(wrapped, this.__chain__); + } + return this.thru(reverse); + } + + /** + * Executes the chain sequence to resolve the unwrapped value. + * + * @name value + * @memberOf _ + * @since 0.1.0 + * @alias toJSON, valueOf + * @category Seq + * @returns {*} Returns the resolved unwrapped value. + * @example + * + * _([1, 2, 3]).value(); + * // => [1, 2, 3] + */ + function wrapperValue() { + return baseWrapperValue(this.__wrapped__, this.__actions__); + } + + /*------------------------------------------------------------------------*/ + + /** + * Creates an object composed of keys generated from the results of running + * each element of `collection` thru `iteratee`. The corresponding value of + * each key is the number of times the key was returned by `iteratee`. The + * iteratee is invoked with one argument: (value). + * + * @static + * @memberOf _ + * @since 0.5.0 + * @category Collection + * @param {Array|Object} collection The collection to iterate over. + * @param {Function} [iteratee=_.identity] The iteratee to transform keys. + * @returns {Object} Returns the composed aggregate object. + * @example + * + * _.countBy([6.1, 4.2, 6.3], Math.floor); + * // => { '4': 1, '6': 2 } + * + * // The `_.property` iteratee shorthand. + * _.countBy(['one', 'two', 'three'], 'length'); + * // => { '3': 2, '5': 1 } + */ + var countBy = createAggregator(function(result, value, key) { + if (hasOwnProperty.call(result, key)) { + ++result[key]; + } else { + baseAssignValue(result, key, 1); + } + }); + + /** + * Checks if `predicate` returns truthy for **all** elements of `collection`. + * Iteration is stopped once `predicate` returns falsey. The predicate is + * invoked with three arguments: (value, index|key, collection). + * + * **Note:** This method returns `true` for + * [empty collections](https://en.wikipedia.org/wiki/Empty_set) because + * [everything is true](https://en.wikipedia.org/wiki/Vacuous_truth) of + * elements of empty collections. + * + * @static + * @memberOf _ + * @since 0.1.0 + * @category Collection + * @param {Array|Object} collection The collection to iterate over. + * @param {Function} [predicate=_.identity] The function invoked per iteration. + * @param- {Object} [guard] Enables use as an iteratee for methods like `_.map`. + * @returns {boolean} Returns `true` if all elements pass the predicate check, + * else `false`. + * @example + * + * _.every([true, 1, null, 'yes'], Boolean); + * // => false + * + * var users = [ + * { 'user': 'barney', 'age': 36, 'active': false }, + * { 'user': 'fred', 'age': 40, 'active': false } + * ]; + * + * // The `_.matches` iteratee shorthand. + * _.every(users, { 'user': 'barney', 'active': false }); + * // => false + * + * // The `_.matchesProperty` iteratee shorthand. + * _.every(users, ['active', false]); + * // => true + * + * // The `_.property` iteratee shorthand. + * _.every(users, 'active'); + * // => false + */ + function every(collection, predicate, guard) { + var func = isArray(collection) ? arrayEvery : baseEvery; + if (guard && isIterateeCall(collection, predicate, guard)) { + predicate = undefined; + } + return func(collection, getIteratee(predicate, 3)); + } + + /** + * Iterates over elements of `collection`, returning an array of all elements + * `predicate` returns truthy for. The predicate is invoked with three + * arguments: (value, index|key, collection). + * + * **Note:** Unlike `_.remove`, this method returns a new array. + * + * @static + * @memberOf _ + * @since 0.1.0 + * @category Collection + * @param {Array|Object} collection The collection to iterate over. + * @param {Function} [predicate=_.identity] The function invoked per iteration. + * @returns {Array} Returns the new filtered array. + * @see _.reject + * @example + * + * var users = [ + * { 'user': 'barney', 'age': 36, 'active': true }, + * { 'user': 'fred', 'age': 40, 'active': false } + * ]; + * + * _.filter(users, function(o) { return !o.active; }); + * // => objects for ['fred'] + * + * // The `_.matches` iteratee shorthand. + * _.filter(users, { 'age': 36, 'active': true }); + * // => objects for ['barney'] + * + * // The `_.matchesProperty` iteratee shorthand. + * _.filter(users, ['active', false]); + * // => objects for ['fred'] + * + * // The `_.property` iteratee shorthand. + * _.filter(users, 'active'); + * // => objects for ['barney'] + * + * // Combining several predicates using `_.overEvery` or `_.overSome`. + * _.filter(users, _.overSome([{ 'age': 36 }, ['age', 40]])); + * // => objects for ['fred', 'barney'] + */ + function filter(collection, predicate) { + var func = isArray(collection) ? arrayFilter : baseFilter; + return func(collection, getIteratee(predicate, 3)); + } + + /** + * Iterates over elements of `collection`, returning the first element + * `predicate` returns truthy for. The predicate is invoked with three + * arguments: (value, index|key, collection). + * + * @static + * @memberOf _ + * @since 0.1.0 + * @category Collection + * @param {Array|Object} collection The collection to inspect. + * @param {Function} [predicate=_.identity] The function invoked per iteration. + * @param {number} [fromIndex=0] The index to search from. + * @returns {*} Returns the matched element, else `undefined`. + * @example + * + * var users = [ + * { 'user': 'barney', 'age': 36, 'active': true }, + * { 'user': 'fred', 'age': 40, 'active': false }, + * { 'user': 'pebbles', 'age': 1, 'active': true } + * ]; + * + * _.find(users, function(o) { return o.age < 40; }); + * // => object for 'barney' + * + * // The `_.matches` iteratee shorthand. + * _.find(users, { 'age': 1, 'active': true }); + * // => object for 'pebbles' + * + * // The `_.matchesProperty` iteratee shorthand. + * _.find(users, ['active', false]); + * // => object for 'fred' + * + * // The `_.property` iteratee shorthand. + * _.find(users, 'active'); + * // => object for 'barney' + */ + var find = createFind(findIndex); + + /** + * This method is like `_.find` except that it iterates over elements of + * `collection` from right to left. + * + * @static + * @memberOf _ + * @since 2.0.0 + * @category Collection + * @param {Array|Object} collection The collection to inspect. + * @param {Function} [predicate=_.identity] The function invoked per iteration. + * @param {number} [fromIndex=collection.length-1] The index to search from. + * @returns {*} Returns the matched element, else `undefined`. + * @example + * + * _.findLast([1, 2, 3, 4], function(n) { + * return n % 2 == 1; + * }); + * // => 3 + */ + var findLast = createFind(findLastIndex); + + /** + * Creates a flattened array of values by running each element in `collection` + * thru `iteratee` and flattening the mapped results. The iteratee is invoked + * with three arguments: (value, index|key, collection). + * + * @static + * @memberOf _ + * @since 4.0.0 + * @category Collection + * @param {Array|Object} collection The collection to iterate over. + * @param {Function} [iteratee=_.identity] The function invoked per iteration. + * @returns {Array} Returns the new flattened array. + * @example + * + * function duplicate(n) { + * return [n, n]; + * } + * + * _.flatMap([1, 2], duplicate); + * // => [1, 1, 2, 2] + */ + function flatMap(collection, iteratee) { + return baseFlatten(map(collection, iteratee), 1); + } + + /** + * This method is like `_.flatMap` except that it recursively flattens the + * mapped results. + * + * @static + * @memberOf _ + * @since 4.7.0 + * @category Collection + * @param {Array|Object} collection The collection to iterate over. + * @param {Function} [iteratee=_.identity] The function invoked per iteration. + * @returns {Array} Returns the new flattened array. + * @example + * + * function duplicate(n) { + * return [[[n, n]]]; + * } + * + * _.flatMapDeep([1, 2], duplicate); + * // => [1, 1, 2, 2] + */ + function flatMapDeep(collection, iteratee) { + return baseFlatten(map(collection, iteratee), INFINITY); + } + + /** + * This method is like `_.flatMap` except that it recursively flattens the + * mapped results up to `depth` times. + * + * @static + * @memberOf _ + * @since 4.7.0 + * @category Collection + * @param {Array|Object} collection The collection to iterate over. + * @param {Function} [iteratee=_.identity] The function invoked per iteration. + * @param {number} [depth=1] The maximum recursion depth. + * @returns {Array} Returns the new flattened array. + * @example + * + * function duplicate(n) { + * return [[[n, n]]]; + * } + * + * _.flatMapDepth([1, 2], duplicate, 2); + * // => [[1, 1], [2, 2]] + */ + function flatMapDepth(collection, iteratee, depth) { + depth = depth === undefined ? 1 : toInteger(depth); + return baseFlatten(map(collection, iteratee), depth); + } + + /** + * Iterates over elements of `collection` and invokes `iteratee` for each element. + * The iteratee is invoked with three arguments: (value, index|key, collection). + * Iteratee functions may exit iteration early by explicitly returning `false`. + * + * **Note:** As with other "Collections" methods, objects with a "length" + * property are iterated like arrays. To avoid this behavior use `_.forIn` + * or `_.forOwn` for object iteration. + * + * @static + * @memberOf _ + * @since 0.1.0 + * @alias each + * @category Collection + * @param {Array|Object} collection The collection to iterate over. + * @param {Function} [iteratee=_.identity] The function invoked per iteration. + * @returns {Array|Object} Returns `collection`. + * @see _.forEachRight + * @example + * + * _.forEach([1, 2], function(value) { + * console.log(value); + * }); + * // => Logs `1` then `2`. + * + * _.forEach({ 'a': 1, 'b': 2 }, function(value, key) { + * console.log(key); + * }); + * // => Logs 'a' then 'b' (iteration order is not guaranteed). + */ + function forEach(collection, iteratee) { + var func = isArray(collection) ? arrayEach : baseEach; + return func(collection, getIteratee(iteratee, 3)); + } + + /** + * This method is like `_.forEach` except that it iterates over elements of + * `collection` from right to left. + * + * @static + * @memberOf _ + * @since 2.0.0 + * @alias eachRight + * @category Collection + * @param {Array|Object} collection The collection to iterate over. + * @param {Function} [iteratee=_.identity] The function invoked per iteration. + * @returns {Array|Object} Returns `collection`. + * @see _.forEach + * @example + * + * _.forEachRight([1, 2], function(value) { + * console.log(value); + * }); + * // => Logs `2` then `1`. + */ + function forEachRight(collection, iteratee) { + var func = isArray(collection) ? arrayEachRight : baseEachRight; + return func(collection, getIteratee(iteratee, 3)); + } + + /** + * Creates an object composed of keys generated from the results of running + * each element of `collection` thru `iteratee`. The order of grouped values + * is determined by the order they occur in `collection`. The corresponding + * value of each key is an array of elements responsible for generating the + * key. The iteratee is invoked with one argument: (value). + * + * @static + * @memberOf _ + * @since 0.1.0 + * @category Collection + * @param {Array|Object} collection The collection to iterate over. + * @param {Function} [iteratee=_.identity] The iteratee to transform keys. + * @returns {Object} Returns the composed aggregate object. + * @example + * + * _.groupBy([6.1, 4.2, 6.3], Math.floor); + * // => { '4': [4.2], '6': [6.1, 6.3] } + * + * // The `_.property` iteratee shorthand. + * _.groupBy(['one', 'two', 'three'], 'length'); + * // => { '3': ['one', 'two'], '5': ['three'] } + */ + var groupBy = createAggregator(function(result, value, key) { + if (hasOwnProperty.call(result, key)) { + result[key].push(value); + } else { + baseAssignValue(result, key, [value]); + } + }); + + /** + * Checks if `value` is in `collection`. If `collection` is a string, it's + * checked for a substring of `value`, otherwise + * [`SameValueZero`](http://ecma-international.org/ecma-262/7.0/#sec-samevaluezero) + * is used for equality comparisons. If `fromIndex` is negative, it's used as + * the offset from the end of `collection`. + * + * @static + * @memberOf _ + * @since 0.1.0 + * @category Collection + * @param {Array|Object|string} collection The collection to inspect. + * @param {*} value The value to search for. + * @param {number} [fromIndex=0] The index to search from. + * @param- {Object} [guard] Enables use as an iteratee for methods like `_.reduce`. + * @returns {boolean} Returns `true` if `value` is found, else `false`. + * @example + * + * _.includes([1, 2, 3], 1); + * // => true + * + * _.includes([1, 2, 3], 1, 2); + * // => false + * + * _.includes({ 'a': 1, 'b': 2 }, 1); + * // => true + * + * _.includes('abcd', 'bc'); + * // => true + */ + function includes(collection, value, fromIndex, guard) { + collection = isArrayLike(collection) ? collection : values(collection); + fromIndex = (fromIndex && !guard) ? toInteger(fromIndex) : 0; + + var length = collection.length; + if (fromIndex < 0) { + fromIndex = nativeMax(length + fromIndex, 0); + } + return isString(collection) + ? (fromIndex <= length && collection.indexOf(value, fromIndex) > -1) + : (!!length && baseIndexOf(collection, value, fromIndex) > -1); + } + + /** + * Invokes the method at `path` of each element in `collection`, returning + * an array of the results of each invoked method. Any additional arguments + * are provided to each invoked method. If `path` is a function, it's invoked + * for, and `this` bound to, each element in `collection`. + * + * @static + * @memberOf _ + * @since 4.0.0 + * @category Collection + * @param {Array|Object} collection The collection to iterate over. + * @param {Array|Function|string} path The path of the method to invoke or + * the function invoked per iteration. + * @param {...*} [args] The arguments to invoke each method with. + * @returns {Array} Returns the array of results. + * @example + * + * _.invokeMap([[5, 1, 7], [3, 2, 1]], 'sort'); + * // => [[1, 5, 7], [1, 2, 3]] + * + * _.invokeMap([123, 456], String.prototype.split, ''); + * // => [['1', '2', '3'], ['4', '5', '6']] + */ + var invokeMap = baseRest(function(collection, path, args) { + var index = -1, + isFunc = typeof path == 'function', + result = isArrayLike(collection) ? Array(collection.length) : []; + + baseEach(collection, function(value) { + result[++index] = isFunc ? apply(path, value, args) : baseInvoke(value, path, args); + }); + return result; + }); + + /** + * Creates an object composed of keys generated from the results of running + * each element of `collection` thru `iteratee`. The corresponding value of + * each key is the last element responsible for generating the key. The + * iteratee is invoked with one argument: (value). + * + * @static + * @memberOf _ + * @since 4.0.0 + * @category Collection + * @param {Array|Object} collection The collection to iterate over. + * @param {Function} [iteratee=_.identity] The iteratee to transform keys. + * @returns {Object} Returns the composed aggregate object. + * @example + * + * var array = [ + * { 'dir': 'left', 'code': 97 }, + * { 'dir': 'right', 'code': 100 } + * ]; + * + * _.keyBy(array, function(o) { + * return String.fromCharCode(o.code); + * }); + * // => { 'a': { 'dir': 'left', 'code': 97 }, 'd': { 'dir': 'right', 'code': 100 } } + * + * _.keyBy(array, 'dir'); + * // => { 'left': { 'dir': 'left', 'code': 97 }, 'right': { 'dir': 'right', 'code': 100 } } + */ + var keyBy = createAggregator(function(result, value, key) { + baseAssignValue(result, key, value); + }); + + /** + * Creates an array of values by running each element in `collection` thru + * `iteratee`. The iteratee is invoked with three arguments: + * (value, index|key, collection). + * + * Many lodash methods are guarded to work as iteratees for methods like + * `_.every`, `_.filter`, `_.map`, `_.mapValues`, `_.reject`, and `_.some`. + * + * The guarded methods are: + * `ary`, `chunk`, `curry`, `curryRight`, `drop`, `dropRight`, `every`, + * `fill`, `invert`, `parseInt`, `random`, `range`, `rangeRight`, `repeat`, + * `sampleSize`, `slice`, `some`, `sortBy`, `split`, `take`, `takeRight`, + * `template`, `trim`, `trimEnd`, `trimStart`, and `words` + * + * @static + * @memberOf _ + * @since 0.1.0 + * @category Collection + * @param {Array|Object} collection The collection to iterate over. + * @param {Function} [iteratee=_.identity] The function invoked per iteration. + * @returns {Array} Returns the new mapped array. + * @example + * + * function square(n) { + * return n * n; + * } + * + * _.map([4, 8], square); + * // => [16, 64] + * + * _.map({ 'a': 4, 'b': 8 }, square); + * // => [16, 64] (iteration order is not guaranteed) + * + * var users = [ + * { 'user': 'barney' }, + * { 'user': 'fred' } + * ]; + * + * // The `_.property` iteratee shorthand. + * _.map(users, 'user'); + * // => ['barney', 'fred'] + */ + function map(collection, iteratee) { + var func = isArray(collection) ? arrayMap : baseMap; + return func(collection, getIteratee(iteratee, 3)); + } + + /** + * This method is like `_.sortBy` except that it allows specifying the sort + * orders of the iteratees to sort by. If `orders` is unspecified, all values + * are sorted in ascending order. Otherwise, specify an order of "desc" for + * descending or "asc" for ascending sort order of corresponding values. + * + * @static + * @memberOf _ + * @since 4.0.0 + * @category Collection + * @param {Array|Object} collection The collection to iterate over. + * @param {Array[]|Function[]|Object[]|string[]} [iteratees=[_.identity]] + * The iteratees to sort by. + * @param {string[]} [orders] The sort orders of `iteratees`. + * @param- {Object} [guard] Enables use as an iteratee for methods like `_.reduce`. + * @returns {Array} Returns the new sorted array. + * @example + * + * var users = [ + * { 'user': 'fred', 'age': 48 }, + * { 'user': 'barney', 'age': 34 }, + * { 'user': 'fred', 'age': 40 }, + * { 'user': 'barney', 'age': 36 } + * ]; + * + * // Sort by `user` in ascending order and by `age` in descending order. + * _.orderBy(users, ['user', 'age'], ['asc', 'desc']); + * // => objects for [['barney', 36], ['barney', 34], ['fred', 48], ['fred', 40]] + */ + function orderBy(collection, iteratees, orders, guard) { + if (collection == null) { + return []; + } + if (!isArray(iteratees)) { + iteratees = iteratees == null ? [] : [iteratees]; + } + orders = guard ? undefined : orders; + if (!isArray(orders)) { + orders = orders == null ? [] : [orders]; + } + return baseOrderBy(collection, iteratees, orders); + } + + /** + * Creates an array of elements split into two groups, the first of which + * contains elements `predicate` returns truthy for, the second of which + * contains elements `predicate` returns falsey for. The predicate is + * invoked with one argument: (value). + * + * @static + * @memberOf _ + * @since 3.0.0 + * @category Collection + * @param {Array|Object} collection The collection to iterate over. + * @param {Function} [predicate=_.identity] The function invoked per iteration. + * @returns {Array} Returns the array of grouped elements. + * @example + * + * var users = [ + * { 'user': 'barney', 'age': 36, 'active': false }, + * { 'user': 'fred', 'age': 40, 'active': true }, + * { 'user': 'pebbles', 'age': 1, 'active': false } + * ]; + * + * _.partition(users, function(o) { return o.active; }); + * // => objects for [['fred'], ['barney', 'pebbles']] + * + * // The `_.matches` iteratee shorthand. + * _.partition(users, { 'age': 1, 'active': false }); + * // => objects for [['pebbles'], ['barney', 'fred']] + * + * // The `_.matchesProperty` iteratee shorthand. + * _.partition(users, ['active', false]); + * // => objects for [['barney', 'pebbles'], ['fred']] + * + * // The `_.property` iteratee shorthand. + * _.partition(users, 'active'); + * // => objects for [['fred'], ['barney', 'pebbles']] + */ + var partition = createAggregator(function(result, value, key) { + result[key ? 0 : 1].push(value); + }, function() { return [[], []]; }); + + /** + * Reduces `collection` to a value which is the accumulated result of running + * each element in `collection` thru `iteratee`, where each successive + * invocation is supplied the return value of the previous. If `accumulator` + * is not given, the first element of `collection` is used as the initial + * value. The iteratee is invoked with four arguments: + * (accumulator, value, index|key, collection). + * + * Many lodash methods are guarded to work as iteratees for methods like + * `_.reduce`, `_.reduceRight`, and `_.transform`. + * + * The guarded methods are: + * `assign`, `defaults`, `defaultsDeep`, `includes`, `merge`, `orderBy`, + * and `sortBy` + * + * @static + * @memberOf _ + * @since 0.1.0 + * @category Collection + * @param {Array|Object} collection The collection to iterate over. + * @param {Function} [iteratee=_.identity] The function invoked per iteration. + * @param {*} [accumulator] The initial value. + * @returns {*} Returns the accumulated value. + * @see _.reduceRight + * @example + * + * _.reduce([1, 2], function(sum, n) { + * return sum + n; + * }, 0); + * // => 3 + * + * _.reduce({ 'a': 1, 'b': 2, 'c': 1 }, function(result, value, key) { + * (result[value] || (result[value] = [])).push(key); + * return result; + * }, {}); + * // => { '1': ['a', 'c'], '2': ['b'] } (iteration order is not guaranteed) + */ + function reduce(collection, iteratee, accumulator) { + var func = isArray(collection) ? arrayReduce : baseReduce, + initAccum = arguments.length < 3; + + return func(collection, getIteratee(iteratee, 4), accumulator, initAccum, baseEach); + } + + /** + * This method is like `_.reduce` except that it iterates over elements of + * `collection` from right to left. + * + * @static + * @memberOf _ + * @since 0.1.0 + * @category Collection + * @param {Array|Object} collection The collection to iterate over. + * @param {Function} [iteratee=_.identity] The function invoked per iteration. + * @param {*} [accumulator] The initial value. + * @returns {*} Returns the accumulated value. + * @see _.reduce + * @example + * + * var array = [[0, 1], [2, 3], [4, 5]]; + * + * _.reduceRight(array, function(flattened, other) { + * return flattened.concat(other); + * }, []); + * // => [4, 5, 2, 3, 0, 1] + */ + function reduceRight(collection, iteratee, accumulator) { + var func = isArray(collection) ? arrayReduceRight : baseReduce, + initAccum = arguments.length < 3; + + return func(collection, getIteratee(iteratee, 4), accumulator, initAccum, baseEachRight); + } + + /** + * The opposite of `_.filter`; this method returns the elements of `collection` + * that `predicate` does **not** return truthy for. + * + * @static + * @memberOf _ + * @since 0.1.0 + * @category Collection + * @param {Array|Object} collection The collection to iterate over. + * @param {Function} [predicate=_.identity] The function invoked per iteration. + * @returns {Array} Returns the new filtered array. + * @see _.filter + * @example + * + * var users = [ + * { 'user': 'barney', 'age': 36, 'active': false }, + * { 'user': 'fred', 'age': 40, 'active': true } + * ]; + * + * _.reject(users, function(o) { return !o.active; }); + * // => objects for ['fred'] + * + * // The `_.matches` iteratee shorthand. + * _.reject(users, { 'age': 40, 'active': true }); + * // => objects for ['barney'] + * + * // The `_.matchesProperty` iteratee shorthand. + * _.reject(users, ['active', false]); + * // => objects for ['fred'] + * + * // The `_.property` iteratee shorthand. + * _.reject(users, 'active'); + * // => objects for ['barney'] + */ + function reject(collection, predicate) { + var func = isArray(collection) ? arrayFilter : baseFilter; + return func(collection, negate(getIteratee(predicate, 3))); + } + + /** + * Gets a random element from `collection`. + * + * @static + * @memberOf _ + * @since 2.0.0 + * @category Collection + * @param {Array|Object} collection The collection to sample. + * @returns {*} Returns the random element. + * @example + * + * _.sample([1, 2, 3, 4]); + * // => 2 + */ + function sample(collection) { + var func = isArray(collection) ? arraySample : baseSample; + return func(collection); + } + + /** + * Gets `n` random elements at unique keys from `collection` up to the + * size of `collection`. + * + * @static + * @memberOf _ + * @since 4.0.0 + * @category Collection + * @param {Array|Object} collection The collection to sample. + * @param {number} [n=1] The number of elements to sample. + * @param- {Object} [guard] Enables use as an iteratee for methods like `_.map`. + * @returns {Array} Returns the random elements. + * @example + * + * _.sampleSize([1, 2, 3], 2); + * // => [3, 1] + * + * _.sampleSize([1, 2, 3], 4); + * // => [2, 3, 1] + */ + function sampleSize(collection, n, guard) { + if ((guard ? isIterateeCall(collection, n, guard) : n === undefined)) { + n = 1; + } else { + n = toInteger(n); + } + var func = isArray(collection) ? arraySampleSize : baseSampleSize; + return func(collection, n); + } + + /** + * Creates an array of shuffled values, using a version of the + * [Fisher-Yates shuffle](https://en.wikipedia.org/wiki/Fisher-Yates_shuffle). + * + * @static + * @memberOf _ + * @since 0.1.0 + * @category Collection + * @param {Array|Object} collection The collection to shuffle. + * @returns {Array} Returns the new shuffled array. + * @example + * + * _.shuffle([1, 2, 3, 4]); + * // => [4, 1, 3, 2] + */ + function shuffle(collection) { + var func = isArray(collection) ? arrayShuffle : baseShuffle; + return func(collection); + } + + /** + * Gets the size of `collection` by returning its length for array-like + * values or the number of own enumerable string keyed properties for objects. + * + * @static + * @memberOf _ + * @since 0.1.0 + * @category Collection + * @param {Array|Object|string} collection The collection to inspect. + * @returns {number} Returns the collection size. + * @example + * + * _.size([1, 2, 3]); + * // => 3 + * + * _.size({ 'a': 1, 'b': 2 }); + * // => 2 + * + * _.size('pebbles'); + * // => 7 + */ + function size(collection) { + if (collection == null) { + return 0; + } + if (isArrayLike(collection)) { + return isString(collection) ? stringSize(collection) : collection.length; + } + var tag = getTag(collection); + if (tag == mapTag || tag == setTag) { + return collection.size; + } + return baseKeys(collection).length; + } + + /** + * Checks if `predicate` returns truthy for **any** element of `collection`. + * Iteration is stopped once `predicate` returns truthy. The predicate is + * invoked with three arguments: (value, index|key, collection). + * + * @static + * @memberOf _ + * @since 0.1.0 + * @category Collection + * @param {Array|Object} collection The collection to iterate over. + * @param {Function} [predicate=_.identity] The function invoked per iteration. + * @param- {Object} [guard] Enables use as an iteratee for methods like `_.map`. + * @returns {boolean} Returns `true` if any element passes the predicate check, + * else `false`. + * @example + * + * _.some([null, 0, 'yes', false], Boolean); + * // => true + * + * var users = [ + * { 'user': 'barney', 'active': true }, + * { 'user': 'fred', 'active': false } + * ]; + * + * // The `_.matches` iteratee shorthand. + * _.some(users, { 'user': 'barney', 'active': false }); + * // => false + * + * // The `_.matchesProperty` iteratee shorthand. + * _.some(users, ['active', false]); + * // => true + * + * // The `_.property` iteratee shorthand. + * _.some(users, 'active'); + * // => true + */ + function some(collection, predicate, guard) { + var func = isArray(collection) ? arraySome : baseSome; + if (guard && isIterateeCall(collection, predicate, guard)) { + predicate = undefined; + } + return func(collection, getIteratee(predicate, 3)); + } + + /** + * Creates an array of elements, sorted in ascending order by the results of + * running each element in a collection thru each iteratee. This method + * performs a stable sort, that is, it preserves the original sort order of + * equal elements. The iteratees are invoked with one argument: (value). + * + * @static + * @memberOf _ + * @since 0.1.0 + * @category Collection + * @param {Array|Object} collection The collection to iterate over. + * @param {...(Function|Function[])} [iteratees=[_.identity]] + * The iteratees to sort by. + * @returns {Array} Returns the new sorted array. + * @example + * + * var users = [ + * { 'user': 'fred', 'age': 48 }, + * { 'user': 'barney', 'age': 36 }, + * { 'user': 'fred', 'age': 30 }, + * { 'user': 'barney', 'age': 34 } + * ]; + * + * _.sortBy(users, [function(o) { return o.user; }]); + * // => objects for [['barney', 36], ['barney', 34], ['fred', 48], ['fred', 30]] + * + * _.sortBy(users, ['user', 'age']); + * // => objects for [['barney', 34], ['barney', 36], ['fred', 30], ['fred', 48]] + */ + var sortBy = baseRest(function(collection, iteratees) { + if (collection == null) { + return []; + } + var length = iteratees.length; + if (length > 1 && isIterateeCall(collection, iteratees[0], iteratees[1])) { + iteratees = []; + } else if (length > 2 && isIterateeCall(iteratees[0], iteratees[1], iteratees[2])) { + iteratees = [iteratees[0]]; + } + return baseOrderBy(collection, baseFlatten(iteratees, 1), []); + }); + + /*------------------------------------------------------------------------*/ + + /** + * Gets the timestamp of the number of milliseconds that have elapsed since + * the Unix epoch (1 January 1970 00:00:00 UTC). + * + * @static + * @memberOf _ + * @since 2.4.0 + * @category Date + * @returns {number} Returns the timestamp. + * @example + * + * _.defer(function(stamp) { + * console.log(_.now() - stamp); + * }, _.now()); + * // => Logs the number of milliseconds it took for the deferred invocation. + */ + var now = ctxNow || function() { + return root.Date.now(); + }; + + /*------------------------------------------------------------------------*/ + + /** + * The opposite of `_.before`; this method creates a function that invokes + * `func` once it's called `n` or more times. + * + * @static + * @memberOf _ + * @since 0.1.0 + * @category Function + * @param {number} n The number of calls before `func` is invoked. + * @param {Function} func The function to restrict. + * @returns {Function} Returns the new restricted function. + * @example + * + * var saves = ['profile', 'settings']; + * + * var done = _.after(saves.length, function() { + * console.log('done saving!'); + * }); + * + * _.forEach(saves, function(type) { + * asyncSave({ 'type': type, 'complete': done }); + * }); + * // => Logs 'done saving!' after the two async saves have completed. + */ + function after(n, func) { + if (typeof func != 'function') { + throw new TypeError(FUNC_ERROR_TEXT); + } + n = toInteger(n); + return function() { + if (--n < 1) { + return func.apply(this, arguments); + } + }; + } + + /** + * Creates a function that invokes `func`, with up to `n` arguments, + * ignoring any additional arguments. + * + * @static + * @memberOf _ + * @since 3.0.0 + * @category Function + * @param {Function} func The function to cap arguments for. + * @param {number} [n=func.length] The arity cap. + * @param- {Object} [guard] Enables use as an iteratee for methods like `_.map`. + * @returns {Function} Returns the new capped function. + * @example + * + * _.map(['6', '8', '10'], _.ary(parseInt, 1)); + * // => [6, 8, 10] + */ + function ary(func, n, guard) { + n = guard ? undefined : n; + n = (func && n == null) ? func.length : n; + return createWrap(func, WRAP_ARY_FLAG, undefined, undefined, undefined, undefined, n); + } + + /** + * Creates a function that invokes `func`, with the `this` binding and arguments + * of the created function, while it's called less than `n` times. Subsequent + * calls to the created function return the result of the last `func` invocation. + * + * @static + * @memberOf _ + * @since 3.0.0 + * @category Function + * @param {number} n The number of calls at which `func` is no longer invoked. + * @param {Function} func The function to restrict. + * @returns {Function} Returns the new restricted function. + * @example + * + * jQuery(element).on('click', _.before(5, addContactToList)); + * // => Allows adding up to 4 contacts to the list. + */ + function before(n, func) { + var result; + if (typeof func != 'function') { + throw new TypeError(FUNC_ERROR_TEXT); + } + n = toInteger(n); + return function() { + if (--n > 0) { + result = func.apply(this, arguments); + } + if (n <= 1) { + func = undefined; + } + return result; + }; + } + + /** + * Creates a function that invokes `func` with the `this` binding of `thisArg` + * and `partials` prepended to the arguments it receives. + * + * The `_.bind.placeholder` value, which defaults to `_` in monolithic builds, + * may be used as a placeholder for partially applied arguments. + * + * **Note:** Unlike native `Function#bind`, this method doesn't set the "length" + * property of bound functions. + * + * @static + * @memberOf _ + * @since 0.1.0 + * @category Function + * @param {Function} func The function to bind. + * @param {*} thisArg The `this` binding of `func`. + * @param {...*} [partials] The arguments to be partially applied. + * @returns {Function} Returns the new bound function. + * @example + * + * function greet(greeting, punctuation) { + * return greeting + ' ' + this.user + punctuation; + * } + * + * var object = { 'user': 'fred' }; + * + * var bound = _.bind(greet, object, 'hi'); + * bound('!'); + * // => 'hi fred!' + * + * // Bound with placeholders. + * var bound = _.bind(greet, object, _, '!'); + * bound('hi'); + * // => 'hi fred!' + */ + var bind = baseRest(function(func, thisArg, partials) { + var bitmask = WRAP_BIND_FLAG; + if (partials.length) { + var holders = replaceHolders(partials, getHolder(bind)); + bitmask |= WRAP_PARTIAL_FLAG; + } + return createWrap(func, bitmask, thisArg, partials, holders); + }); + + /** + * Creates a function that invokes the method at `object[key]` with `partials` + * prepended to the arguments it receives. + * + * This method differs from `_.bind` by allowing bound functions to reference + * methods that may be redefined or don't yet exist. See + * [Peter Michaux's article](http://peter.michaux.ca/articles/lazy-function-definition-pattern) + * for more details. + * + * The `_.bindKey.placeholder` value, which defaults to `_` in monolithic + * builds, may be used as a placeholder for partially applied arguments. + * + * @static + * @memberOf _ + * @since 0.10.0 + * @category Function + * @param {Object} object The object to invoke the method on. + * @param {string} key The key of the method. + * @param {...*} [partials] The arguments to be partially applied. + * @returns {Function} Returns the new bound function. + * @example + * + * var object = { + * 'user': 'fred', + * 'greet': function(greeting, punctuation) { + * return greeting + ' ' + this.user + punctuation; + * } + * }; + * + * var bound = _.bindKey(object, 'greet', 'hi'); + * bound('!'); + * // => 'hi fred!' + * + * object.greet = function(greeting, punctuation) { + * return greeting + 'ya ' + this.user + punctuation; + * }; + * + * bound('!'); + * // => 'hiya fred!' + * + * // Bound with placeholders. + * var bound = _.bindKey(object, 'greet', _, '!'); + * bound('hi'); + * // => 'hiya fred!' + */ + var bindKey = baseRest(function(object, key, partials) { + var bitmask = WRAP_BIND_FLAG | WRAP_BIND_KEY_FLAG; + if (partials.length) { + var holders = replaceHolders(partials, getHolder(bindKey)); + bitmask |= WRAP_PARTIAL_FLAG; + } + return createWrap(key, bitmask, object, partials, holders); + }); + + /** + * Creates a function that accepts arguments of `func` and either invokes + * `func` returning its result, if at least `arity` number of arguments have + * been provided, or returns a function that accepts the remaining `func` + * arguments, and so on. The arity of `func` may be specified if `func.length` + * is not sufficient. + * + * The `_.curry.placeholder` value, which defaults to `_` in monolithic builds, + * may be used as a placeholder for provided arguments. + * + * **Note:** This method doesn't set the "length" property of curried functions. + * + * @static + * @memberOf _ + * @since 2.0.0 + * @category Function + * @param {Function} func The function to curry. + * @param {number} [arity=func.length] The arity of `func`. + * @param- {Object} [guard] Enables use as an iteratee for methods like `_.map`. + * @returns {Function} Returns the new curried function. + * @example + * + * var abc = function(a, b, c) { + * return [a, b, c]; + * }; + * + * var curried = _.curry(abc); + * + * curried(1)(2)(3); + * // => [1, 2, 3] + * + * curried(1, 2)(3); + * // => [1, 2, 3] + * + * curried(1, 2, 3); + * // => [1, 2, 3] + * + * // Curried with placeholders. + * curried(1)(_, 3)(2); + * // => [1, 2, 3] + */ + function curry(func, arity, guard) { + arity = guard ? undefined : arity; + var result = createWrap(func, WRAP_CURRY_FLAG, undefined, undefined, undefined, undefined, undefined, arity); + result.placeholder = curry.placeholder; + return result; + } + + /** + * This method is like `_.curry` except that arguments are applied to `func` + * in the manner of `_.partialRight` instead of `_.partial`. + * + * The `_.curryRight.placeholder` value, which defaults to `_` in monolithic + * builds, may be used as a placeholder for provided arguments. + * + * **Note:** This method doesn't set the "length" property of curried functions. + * + * @static + * @memberOf _ + * @since 3.0.0 + * @category Function + * @param {Function} func The function to curry. + * @param {number} [arity=func.length] The arity of `func`. + * @param- {Object} [guard] Enables use as an iteratee for methods like `_.map`. + * @returns {Function} Returns the new curried function. + * @example + * + * var abc = function(a, b, c) { + * return [a, b, c]; + * }; + * + * var curried = _.curryRight(abc); + * + * curried(3)(2)(1); + * // => [1, 2, 3] + * + * curried(2, 3)(1); + * // => [1, 2, 3] + * + * curried(1, 2, 3); + * // => [1, 2, 3] + * + * // Curried with placeholders. + * curried(3)(1, _)(2); + * // => [1, 2, 3] + */ + function curryRight(func, arity, guard) { + arity = guard ? undefined : arity; + var result = createWrap(func, WRAP_CURRY_RIGHT_FLAG, undefined, undefined, undefined, undefined, undefined, arity); + result.placeholder = curryRight.placeholder; + return result; + } + + /** + * Creates a debounced function that delays invoking `func` until after `wait` + * milliseconds have elapsed since the last time the debounced function was + * invoked. The debounced function comes with a `cancel` method to cancel + * delayed `func` invocations and a `flush` method to immediately invoke them. + * Provide `options` to indicate whether `func` should be invoked on the + * leading and/or trailing edge of the `wait` timeout. The `func` is invoked + * with the last arguments provided to the debounced function. Subsequent + * calls to the debounced function return the result of the last `func` + * invocation. + * + * **Note:** If `leading` and `trailing` options are `true`, `func` is + * invoked on the trailing edge of the timeout only if the debounced function + * is invoked more than once during the `wait` timeout. + * + * If `wait` is `0` and `leading` is `false`, `func` invocation is deferred + * until to the next tick, similar to `setTimeout` with a timeout of `0`. + * + * See [David Corbacho's article](https://css-tricks.com/debouncing-throttling-explained-examples/) + * for details over the differences between `_.debounce` and `_.throttle`. + * + * @static + * @memberOf _ + * @since 0.1.0 + * @category Function + * @param {Function} func The function to debounce. + * @param {number} [wait=0] The number of milliseconds to delay. + * @param {Object} [options={}] The options object. + * @param {boolean} [options.leading=false] + * Specify invoking on the leading edge of the timeout. + * @param {number} [options.maxWait] + * The maximum time `func` is allowed to be delayed before it's invoked. + * @param {boolean} [options.trailing=true] + * Specify invoking on the trailing edge of the timeout. + * @returns {Function} Returns the new debounced function. + * @example + * + * // Avoid costly calculations while the window size is in flux. + * jQuery(window).on('resize', _.debounce(calculateLayout, 150)); + * + * // Invoke `sendMail` when clicked, debouncing subsequent calls. + * jQuery(element).on('click', _.debounce(sendMail, 300, { + * 'leading': true, + * 'trailing': false + * })); + * + * // Ensure `batchLog` is invoked once after 1 second of debounced calls. + * var debounced = _.debounce(batchLog, 250, { 'maxWait': 1000 }); + * var source = new EventSource('/stream'); + * jQuery(source).on('message', debounced); + * + * // Cancel the trailing debounced invocation. + * jQuery(window).on('popstate', debounced.cancel); + */ + function debounce(func, wait, options) { + var lastArgs, + lastThis, + maxWait, + result, + timerId, + lastCallTime, + lastInvokeTime = 0, + leading = false, + maxing = false, + trailing = true; + + if (typeof func != 'function') { + throw new TypeError(FUNC_ERROR_TEXT); + } + wait = toNumber(wait) || 0; + if (isObject(options)) { + leading = !!options.leading; + maxing = 'maxWait' in options; + maxWait = maxing ? nativeMax(toNumber(options.maxWait) || 0, wait) : maxWait; + trailing = 'trailing' in options ? !!options.trailing : trailing; + } + + function invokeFunc(time) { + var args = lastArgs, + thisArg = lastThis; + + lastArgs = lastThis = undefined; + lastInvokeTime = time; + result = func.apply(thisArg, args); + return result; + } + + function leadingEdge(time) { + // Reset any `maxWait` timer. + lastInvokeTime = time; + // Start the timer for the trailing edge. + timerId = setTimeout(timerExpired, wait); + // Invoke the leading edge. + return leading ? invokeFunc(time) : result; + } + + function remainingWait(time) { + var timeSinceLastCall = time - lastCallTime, + timeSinceLastInvoke = time - lastInvokeTime, + timeWaiting = wait - timeSinceLastCall; + + return maxing + ? nativeMin(timeWaiting, maxWait - timeSinceLastInvoke) + : timeWaiting; + } + + function shouldInvoke(time) { + var timeSinceLastCall = time - lastCallTime, + timeSinceLastInvoke = time - lastInvokeTime; + + // Either this is the first call, activity has stopped and we're at the + // trailing edge, the system time has gone backwards and we're treating + // it as the trailing edge, or we've hit the `maxWait` limit. + return (lastCallTime === undefined || (timeSinceLastCall >= wait) || + (timeSinceLastCall < 0) || (maxing && timeSinceLastInvoke >= maxWait)); + } + + function timerExpired() { + var time = now(); + if (shouldInvoke(time)) { + return trailingEdge(time); + } + // Restart the timer. + timerId = setTimeout(timerExpired, remainingWait(time)); + } + + function trailingEdge(time) { + timerId = undefined; + + // Only invoke if we have `lastArgs` which means `func` has been + // debounced at least once. + if (trailing && lastArgs) { + return invokeFunc(time); + } + lastArgs = lastThis = undefined; + return result; + } + + function cancel() { + if (timerId !== undefined) { + clearTimeout(timerId); + } + lastInvokeTime = 0; + lastArgs = lastCallTime = lastThis = timerId = undefined; + } + + function flush() { + return timerId === undefined ? result : trailingEdge(now()); + } + + function debounced() { + var time = now(), + isInvoking = shouldInvoke(time); + + lastArgs = arguments; + lastThis = this; + lastCallTime = time; + + if (isInvoking) { + if (timerId === undefined) { + return leadingEdge(lastCallTime); + } + if (maxing) { + // Handle invocations in a tight loop. + clearTimeout(timerId); + timerId = setTimeout(timerExpired, wait); + return invokeFunc(lastCallTime); + } + } + if (timerId === undefined) { + timerId = setTimeout(timerExpired, wait); + } + return result; + } + debounced.cancel = cancel; + debounced.flush = flush; + return debounced; + } + + /** + * Defers invoking the `func` until the current call stack has cleared. Any + * additional arguments are provided to `func` when it's invoked. + * + * @static + * @memberOf _ + * @since 0.1.0 + * @category Function + * @param {Function} func The function to defer. + * @param {...*} [args] The arguments to invoke `func` with. + * @returns {number} Returns the timer id. + * @example + * + * _.defer(function(text) { + * console.log(text); + * }, 'deferred'); + * // => Logs 'deferred' after one millisecond. + */ + var defer = baseRest(function(func, args) { + return baseDelay(func, 1, args); + }); + + /** + * Invokes `func` after `wait` milliseconds. Any additional arguments are + * provided to `func` when it's invoked. + * + * @static + * @memberOf _ + * @since 0.1.0 + * @category Function + * @param {Function} func The function to delay. + * @param {number} wait The number of milliseconds to delay invocation. + * @param {...*} [args] The arguments to invoke `func` with. + * @returns {number} Returns the timer id. + * @example + * + * _.delay(function(text) { + * console.log(text); + * }, 1000, 'later'); + * // => Logs 'later' after one second. + */ + var delay = baseRest(function(func, wait, args) { + return baseDelay(func, toNumber(wait) || 0, args); + }); + + /** + * Creates a function that invokes `func` with arguments reversed. + * + * @static + * @memberOf _ + * @since 4.0.0 + * @category Function + * @param {Function} func The function to flip arguments for. + * @returns {Function} Returns the new flipped function. + * @example + * + * var flipped = _.flip(function() { + * return _.toArray(arguments); + * }); + * + * flipped('a', 'b', 'c', 'd'); + * // => ['d', 'c', 'b', 'a'] + */ + function flip(func) { + return createWrap(func, WRAP_FLIP_FLAG); + } + + /** + * Creates a function that memoizes the result of `func`. If `resolver` is + * provided, it determines the cache key for storing the result based on the + * arguments provided to the memoized function. By default, the first argument + * provided to the memoized function is used as the map cache key. The `func` + * is invoked with the `this` binding of the memoized function. + * + * **Note:** The cache is exposed as the `cache` property on the memoized + * function. Its creation may be customized by replacing the `_.memoize.Cache` + * constructor with one whose instances implement the + * [`Map`](http://ecma-international.org/ecma-262/7.0/#sec-properties-of-the-map-prototype-object) + * method interface of `clear`, `delete`, `get`, `has`, and `set`. + * + * @static + * @memberOf _ + * @since 0.1.0 + * @category Function + * @param {Function} func The function to have its output memoized. + * @param {Function} [resolver] The function to resolve the cache key. + * @returns {Function} Returns the new memoized function. + * @example + * + * var object = { 'a': 1, 'b': 2 }; + * var other = { 'c': 3, 'd': 4 }; + * + * var values = _.memoize(_.values); + * values(object); + * // => [1, 2] + * + * values(other); + * // => [3, 4] + * + * object.a = 2; + * values(object); + * // => [1, 2] + * + * // Modify the result cache. + * values.cache.set(object, ['a', 'b']); + * values(object); + * // => ['a', 'b'] + * + * // Replace `_.memoize.Cache`. + * _.memoize.Cache = WeakMap; + */ + function memoize(func, resolver) { + if (typeof func != 'function' || (resolver != null && typeof resolver != 'function')) { + throw new TypeError(FUNC_ERROR_TEXT); + } + var memoized = function() { + var args = arguments, + key = resolver ? resolver.apply(this, args) : args[0], + cache = memoized.cache; + + if (cache.has(key)) { + return cache.get(key); + } + var result = func.apply(this, args); + memoized.cache = cache.set(key, result) || cache; + return result; + }; + memoized.cache = new (memoize.Cache || MapCache); + return memoized; + } + + // Expose `MapCache`. + memoize.Cache = MapCache; + + /** + * Creates a function that negates the result of the predicate `func`. The + * `func` predicate is invoked with the `this` binding and arguments of the + * created function. + * + * @static + * @memberOf _ + * @since 3.0.0 + * @category Function + * @param {Function} predicate The predicate to negate. + * @returns {Function} Returns the new negated function. + * @example + * + * function isEven(n) { + * return n % 2 == 0; + * } + * + * _.filter([1, 2, 3, 4, 5, 6], _.negate(isEven)); + * // => [1, 3, 5] + */ + function negate(predicate) { + if (typeof predicate != 'function') { + throw new TypeError(FUNC_ERROR_TEXT); + } + return function() { + var args = arguments; + switch (args.length) { + case 0: return !predicate.call(this); + case 1: return !predicate.call(this, args[0]); + case 2: return !predicate.call(this, args[0], args[1]); + case 3: return !predicate.call(this, args[0], args[1], args[2]); + } + return !predicate.apply(this, args); + }; + } + + /** + * Creates a function that is restricted to invoking `func` once. Repeat calls + * to the function return the value of the first invocation. The `func` is + * invoked with the `this` binding and arguments of the created function. + * + * @static + * @memberOf _ + * @since 0.1.0 + * @category Function + * @param {Function} func The function to restrict. + * @returns {Function} Returns the new restricted function. + * @example + * + * var initialize = _.once(createApplication); + * initialize(); + * initialize(); + * // => `createApplication` is invoked once + */ + function once(func) { + return before(2, func); + } + + /** + * Creates a function that invokes `func` with its arguments transformed. + * + * @static + * @since 4.0.0 + * @memberOf _ + * @category Function + * @param {Function} func The function to wrap. + * @param {...(Function|Function[])} [transforms=[_.identity]] + * The argument transforms. + * @returns {Function} Returns the new function. + * @example + * + * function doubled(n) { + * return n * 2; + * } + * + * function square(n) { + * return n * n; + * } + * + * var func = _.overArgs(function(x, y) { + * return [x, y]; + * }, [square, doubled]); + * + * func(9, 3); + * // => [81, 6] + * + * func(10, 5); + * // => [100, 10] + */ + var overArgs = castRest(function(func, transforms) { + transforms = (transforms.length == 1 && isArray(transforms[0])) + ? arrayMap(transforms[0], baseUnary(getIteratee())) + : arrayMap(baseFlatten(transforms, 1), baseUnary(getIteratee())); + + var funcsLength = transforms.length; + return baseRest(function(args) { + var index = -1, + length = nativeMin(args.length, funcsLength); + + while (++index < length) { + args[index] = transforms[index].call(this, args[index]); + } + return apply(func, this, args); + }); + }); + + /** + * Creates a function that invokes `func` with `partials` prepended to the + * arguments it receives. This method is like `_.bind` except it does **not** + * alter the `this` binding. + * + * The `_.partial.placeholder` value, which defaults to `_` in monolithic + * builds, may be used as a placeholder for partially applied arguments. + * + * **Note:** This method doesn't set the "length" property of partially + * applied functions. + * + * @static + * @memberOf _ + * @since 0.2.0 + * @category Function + * @param {Function} func The function to partially apply arguments to. + * @param {...*} [partials] The arguments to be partially applied. + * @returns {Function} Returns the new partially applied function. + * @example + * + * function greet(greeting, name) { + * return greeting + ' ' + name; + * } + * + * var sayHelloTo = _.partial(greet, 'hello'); + * sayHelloTo('fred'); + * // => 'hello fred' + * + * // Partially applied with placeholders. + * var greetFred = _.partial(greet, _, 'fred'); + * greetFred('hi'); + * // => 'hi fred' + */ + var partial = baseRest(function(func, partials) { + var holders = replaceHolders(partials, getHolder(partial)); + return createWrap(func, WRAP_PARTIAL_FLAG, undefined, partials, holders); + }); + + /** + * This method is like `_.partial` except that partially applied arguments + * are appended to the arguments it receives. + * + * The `_.partialRight.placeholder` value, which defaults to `_` in monolithic + * builds, may be used as a placeholder for partially applied arguments. + * + * **Note:** This method doesn't set the "length" property of partially + * applied functions. + * + * @static + * @memberOf _ + * @since 1.0.0 + * @category Function + * @param {Function} func The function to partially apply arguments to. + * @param {...*} [partials] The arguments to be partially applied. + * @returns {Function} Returns the new partially applied function. + * @example + * + * function greet(greeting, name) { + * return greeting + ' ' + name; + * } + * + * var greetFred = _.partialRight(greet, 'fred'); + * greetFred('hi'); + * // => 'hi fred' + * + * // Partially applied with placeholders. + * var sayHelloTo = _.partialRight(greet, 'hello', _); + * sayHelloTo('fred'); + * // => 'hello fred' + */ + var partialRight = baseRest(function(func, partials) { + var holders = replaceHolders(partials, getHolder(partialRight)); + return createWrap(func, WRAP_PARTIAL_RIGHT_FLAG, undefined, partials, holders); + }); + + /** + * Creates a function that invokes `func` with arguments arranged according + * to the specified `indexes` where the argument value at the first index is + * provided as the first argument, the argument value at the second index is + * provided as the second argument, and so on. + * + * @static + * @memberOf _ + * @since 3.0.0 + * @category Function + * @param {Function} func The function to rearrange arguments for. + * @param {...(number|number[])} indexes The arranged argument indexes. + * @returns {Function} Returns the new function. + * @example + * + * var rearged = _.rearg(function(a, b, c) { + * return [a, b, c]; + * }, [2, 0, 1]); + * + * rearged('b', 'c', 'a') + * // => ['a', 'b', 'c'] + */ + var rearg = flatRest(function(func, indexes) { + return createWrap(func, WRAP_REARG_FLAG, undefined, undefined, undefined, indexes); + }); + + /** + * Creates a function that invokes `func` with the `this` binding of the + * created function and arguments from `start` and beyond provided as + * an array. + * + * **Note:** This method is based on the + * [rest parameter](https://mdn.io/rest_parameters). + * + * @static + * @memberOf _ + * @since 4.0.0 + * @category Function + * @param {Function} func The function to apply a rest parameter to. + * @param {number} [start=func.length-1] The start position of the rest parameter. + * @returns {Function} Returns the new function. + * @example + * + * var say = _.rest(function(what, names) { + * return what + ' ' + _.initial(names).join(', ') + + * (_.size(names) > 1 ? ', & ' : '') + _.last(names); + * }); + * + * say('hello', 'fred', 'barney', 'pebbles'); + * // => 'hello fred, barney, & pebbles' + */ + function rest(func, start) { + if (typeof func != 'function') { + throw new TypeError(FUNC_ERROR_TEXT); + } + start = start === undefined ? start : toInteger(start); + return baseRest(func, start); + } + + /** + * Creates a function that invokes `func` with the `this` binding of the + * create function and an array of arguments much like + * [`Function#apply`](http://www.ecma-international.org/ecma-262/7.0/#sec-function.prototype.apply). + * + * **Note:** This method is based on the + * [spread operator](https://mdn.io/spread_operator). + * + * @static + * @memberOf _ + * @since 3.2.0 + * @category Function + * @param {Function} func The function to spread arguments over. + * @param {number} [start=0] The start position of the spread. + * @returns {Function} Returns the new function. + * @example + * + * var say = _.spread(function(who, what) { + * return who + ' says ' + what; + * }); + * + * say(['fred', 'hello']); + * // => 'fred says hello' + * + * var numbers = Promise.all([ + * Promise.resolve(40), + * Promise.resolve(36) + * ]); + * + * numbers.then(_.spread(function(x, y) { + * return x + y; + * })); + * // => a Promise of 76 + */ + function spread(func, start) { + if (typeof func != 'function') { + throw new TypeError(FUNC_ERROR_TEXT); + } + start = start == null ? 0 : nativeMax(toInteger(start), 0); + return baseRest(function(args) { + var array = args[start], + otherArgs = castSlice(args, 0, start); + + if (array) { + arrayPush(otherArgs, array); + } + return apply(func, this, otherArgs); + }); + } + + /** + * Creates a throttled function that only invokes `func` at most once per + * every `wait` milliseconds. The throttled function comes with a `cancel` + * method to cancel delayed `func` invocations and a `flush` method to + * immediately invoke them. Provide `options` to indicate whether `func` + * should be invoked on the leading and/or trailing edge of the `wait` + * timeout. The `func` is invoked with the last arguments provided to the + * throttled function. Subsequent calls to the throttled function return the + * result of the last `func` invocation. + * + * **Note:** If `leading` and `trailing` options are `true`, `func` is + * invoked on the trailing edge of the timeout only if the throttled function + * is invoked more than once during the `wait` timeout. + * + * If `wait` is `0` and `leading` is `false`, `func` invocation is deferred + * until to the next tick, similar to `setTimeout` with a timeout of `0`. + * + * See [David Corbacho's article](https://css-tricks.com/debouncing-throttling-explained-examples/) + * for details over the differences between `_.throttle` and `_.debounce`. + * + * @static + * @memberOf _ + * @since 0.1.0 + * @category Function + * @param {Function} func The function to throttle. + * @param {number} [wait=0] The number of milliseconds to throttle invocations to. + * @param {Object} [options={}] The options object. + * @param {boolean} [options.leading=true] + * Specify invoking on the leading edge of the timeout. + * @param {boolean} [options.trailing=true] + * Specify invoking on the trailing edge of the timeout. + * @returns {Function} Returns the new throttled function. + * @example + * + * // Avoid excessively updating the position while scrolling. + * jQuery(window).on('scroll', _.throttle(updatePosition, 100)); + * + * // Invoke `renewToken` when the click event is fired, but not more than once every 5 minutes. + * var throttled = _.throttle(renewToken, 300000, { 'trailing': false }); + * jQuery(element).on('click', throttled); + * + * // Cancel the trailing throttled invocation. + * jQuery(window).on('popstate', throttled.cancel); + */ + function throttle(func, wait, options) { + var leading = true, + trailing = true; + + if (typeof func != 'function') { + throw new TypeError(FUNC_ERROR_TEXT); + } + if (isObject(options)) { + leading = 'leading' in options ? !!options.leading : leading; + trailing = 'trailing' in options ? !!options.trailing : trailing; + } + return debounce(func, wait, { + 'leading': leading, + 'maxWait': wait, + 'trailing': trailing + }); + } + + /** + * Creates a function that accepts up to one argument, ignoring any + * additional arguments. + * + * @static + * @memberOf _ + * @since 4.0.0 + * @category Function + * @param {Function} func The function to cap arguments for. + * @returns {Function} Returns the new capped function. + * @example + * + * _.map(['6', '8', '10'], _.unary(parseInt)); + * // => [6, 8, 10] + */ + function unary(func) { + return ary(func, 1); + } + + /** + * Creates a function that provides `value` to `wrapper` as its first + * argument. Any additional arguments provided to the function are appended + * to those provided to the `wrapper`. The wrapper is invoked with the `this` + * binding of the created function. + * + * @static + * @memberOf _ + * @since 0.1.0 + * @category Function + * @param {*} value The value to wrap. + * @param {Function} [wrapper=identity] The wrapper function. + * @returns {Function} Returns the new function. + * @example + * + * var p = _.wrap(_.escape, function(func, text) { + * return '

' + func(text) + '

'; + * }); + * + * p('fred, barney, & pebbles'); + * // => '

fred, barney, & pebbles

' + */ + function wrap(value, wrapper) { + return partial(castFunction(wrapper), value); + } + + /*------------------------------------------------------------------------*/ + + /** + * Casts `value` as an array if it's not one. + * + * @static + * @memberOf _ + * @since 4.4.0 + * @category Lang + * @param {*} value The value to inspect. + * @returns {Array} Returns the cast array. + * @example + * + * _.castArray(1); + * // => [1] + * + * _.castArray({ 'a': 1 }); + * // => [{ 'a': 1 }] + * + * _.castArray('abc'); + * // => ['abc'] + * + * _.castArray(null); + * // => [null] + * + * _.castArray(undefined); + * // => [undefined] + * + * _.castArray(); + * // => [] + * + * var array = [1, 2, 3]; + * console.log(_.castArray(array) === array); + * // => true + */ + function castArray() { + if (!arguments.length) { + return []; + } + var value = arguments[0]; + return isArray(value) ? value : [value]; + } + + /** + * Creates a shallow clone of `value`. + * + * **Note:** This method is loosely based on the + * [structured clone algorithm](https://mdn.io/Structured_clone_algorithm) + * and supports cloning arrays, array buffers, booleans, date objects, maps, + * numbers, `Object` objects, regexes, sets, strings, symbols, and typed + * arrays. The own enumerable properties of `arguments` objects are cloned + * as plain objects. An empty object is returned for uncloneable values such + * as error objects, functions, DOM nodes, and WeakMaps. + * + * @static + * @memberOf _ + * @since 0.1.0 + * @category Lang + * @param {*} value The value to clone. + * @returns {*} Returns the cloned value. + * @see _.cloneDeep + * @example + * + * var objects = [{ 'a': 1 }, { 'b': 2 }]; + * + * var shallow = _.clone(objects); + * console.log(shallow[0] === objects[0]); + * // => true + */ + function clone(value) { + return baseClone(value, CLONE_SYMBOLS_FLAG); + } + + /** + * This method is like `_.clone` except that it accepts `customizer` which + * is invoked to produce the cloned value. If `customizer` returns `undefined`, + * cloning is handled by the method instead. The `customizer` is invoked with + * up to four arguments; (value [, index|key, object, stack]). + * + * @static + * @memberOf _ + * @since 4.0.0 + * @category Lang + * @param {*} value The value to clone. + * @param {Function} [customizer] The function to customize cloning. + * @returns {*} Returns the cloned value. + * @see _.cloneDeepWith + * @example + * + * function customizer(value) { + * if (_.isElement(value)) { + * return value.cloneNode(false); + * } + * } + * + * var el = _.cloneWith(document.body, customizer); + * + * console.log(el === document.body); + * // => false + * console.log(el.nodeName); + * // => 'BODY' + * console.log(el.childNodes.length); + * // => 0 + */ + function cloneWith(value, customizer) { + customizer = typeof customizer == 'function' ? customizer : undefined; + return baseClone(value, CLONE_SYMBOLS_FLAG, customizer); + } + + /** + * This method is like `_.clone` except that it recursively clones `value`. + * + * @static + * @memberOf _ + * @since 1.0.0 + * @category Lang + * @param {*} value The value to recursively clone. + * @returns {*} Returns the deep cloned value. + * @see _.clone + * @example + * + * var objects = [{ 'a': 1 }, { 'b': 2 }]; + * + * var deep = _.cloneDeep(objects); + * console.log(deep[0] === objects[0]); + * // => false + */ + function cloneDeep(value) { + return baseClone(value, CLONE_DEEP_FLAG | CLONE_SYMBOLS_FLAG); + } + + /** + * This method is like `_.cloneWith` except that it recursively clones `value`. + * + * @static + * @memberOf _ + * @since 4.0.0 + * @category Lang + * @param {*} value The value to recursively clone. + * @param {Function} [customizer] The function to customize cloning. + * @returns {*} Returns the deep cloned value. + * @see _.cloneWith + * @example + * + * function customizer(value) { + * if (_.isElement(value)) { + * return value.cloneNode(true); + * } + * } + * + * var el = _.cloneDeepWith(document.body, customizer); + * + * console.log(el === document.body); + * // => false + * console.log(el.nodeName); + * // => 'BODY' + * console.log(el.childNodes.length); + * // => 20 + */ + function cloneDeepWith(value, customizer) { + customizer = typeof customizer == 'function' ? customizer : undefined; + return baseClone(value, CLONE_DEEP_FLAG | CLONE_SYMBOLS_FLAG, customizer); + } + + /** + * Checks if `object` conforms to `source` by invoking the predicate + * properties of `source` with the corresponding property values of `object`. + * + * **Note:** This method is equivalent to `_.conforms` when `source` is + * partially applied. + * + * @static + * @memberOf _ + * @since 4.14.0 + * @category Lang + * @param {Object} object The object to inspect. + * @param {Object} source The object of property predicates to conform to. + * @returns {boolean} Returns `true` if `object` conforms, else `false`. + * @example + * + * var object = { 'a': 1, 'b': 2 }; + * + * _.conformsTo(object, { 'b': function(n) { return n > 1; } }); + * // => true + * + * _.conformsTo(object, { 'b': function(n) { return n > 2; } }); + * // => false + */ + function conformsTo(object, source) { + return source == null || baseConformsTo(object, source, keys(source)); + } + + /** + * Performs a + * [`SameValueZero`](http://ecma-international.org/ecma-262/7.0/#sec-samevaluezero) + * comparison between two values to determine if they are equivalent. + * + * @static + * @memberOf _ + * @since 4.0.0 + * @category Lang + * @param {*} value The value to compare. + * @param {*} other The other value to compare. + * @returns {boolean} Returns `true` if the values are equivalent, else `false`. + * @example + * + * var object = { 'a': 1 }; + * var other = { 'a': 1 }; + * + * _.eq(object, object); + * // => true + * + * _.eq(object, other); + * // => false + * + * _.eq('a', 'a'); + * // => true + * + * _.eq('a', Object('a')); + * // => false + * + * _.eq(NaN, NaN); + * // => true + */ + function eq(value, other) { + return value === other || (value !== value && other !== other); + } + + /** + * Checks if `value` is greater than `other`. + * + * @static + * @memberOf _ + * @since 3.9.0 + * @category Lang + * @param {*} value The value to compare. + * @param {*} other The other value to compare. + * @returns {boolean} Returns `true` if `value` is greater than `other`, + * else `false`. + * @see _.lt + * @example + * + * _.gt(3, 1); + * // => true + * + * _.gt(3, 3); + * // => false + * + * _.gt(1, 3); + * // => false + */ + var gt = createRelationalOperation(baseGt); + + /** + * Checks if `value` is greater than or equal to `other`. + * + * @static + * @memberOf _ + * @since 3.9.0 + * @category Lang + * @param {*} value The value to compare. + * @param {*} other The other value to compare. + * @returns {boolean} Returns `true` if `value` is greater than or equal to + * `other`, else `false`. + * @see _.lte + * @example + * + * _.gte(3, 1); + * // => true + * + * _.gte(3, 3); + * // => true + * + * _.gte(1, 3); + * // => false + */ + var gte = createRelationalOperation(function(value, other) { + return value >= other; + }); + + /** + * Checks if `value` is likely an `arguments` object. + * + * @static + * @memberOf _ + * @since 0.1.0 + * @category Lang + * @param {*} value The value to check. + * @returns {boolean} Returns `true` if `value` is an `arguments` object, + * else `false`. + * @example + * + * _.isArguments(function() { return arguments; }()); + * // => true + * + * _.isArguments([1, 2, 3]); + * // => false + */ + var isArguments = baseIsArguments(function() { return arguments; }()) ? baseIsArguments : function(value) { + return isObjectLike(value) && hasOwnProperty.call(value, 'callee') && + !propertyIsEnumerable.call(value, 'callee'); + }; + + /** + * Checks if `value` is classified as an `Array` object. + * + * @static + * @memberOf _ + * @since 0.1.0 + * @category Lang + * @param {*} value The value to check. + * @returns {boolean} Returns `true` if `value` is an array, else `false`. + * @example + * + * _.isArray([1, 2, 3]); + * // => true + * + * _.isArray(document.body.children); + * // => false + * + * _.isArray('abc'); + * // => false + * + * _.isArray(_.noop); + * // => false + */ + var isArray = Array.isArray; + + /** + * Checks if `value` is classified as an `ArrayBuffer` object. + * + * @static + * @memberOf _ + * @since 4.3.0 + * @category Lang + * @param {*} value The value to check. + * @returns {boolean} Returns `true` if `value` is an array buffer, else `false`. + * @example + * + * _.isArrayBuffer(new ArrayBuffer(2)); + * // => true + * + * _.isArrayBuffer(new Array(2)); + * // => false + */ + var isArrayBuffer = nodeIsArrayBuffer ? baseUnary(nodeIsArrayBuffer) : baseIsArrayBuffer; + + /** + * Checks if `value` is array-like. A value is considered array-like if it's + * not a function and has a `value.length` that's an integer greater than or + * equal to `0` and less than or equal to `Number.MAX_SAFE_INTEGER`. + * + * @static + * @memberOf _ + * @since 4.0.0 + * @category Lang + * @param {*} value The value to check. + * @returns {boolean} Returns `true` if `value` is array-like, else `false`. + * @example + * + * _.isArrayLike([1, 2, 3]); + * // => true + * + * _.isArrayLike(document.body.children); + * // => true + * + * _.isArrayLike('abc'); + * // => true + * + * _.isArrayLike(_.noop); + * // => false + */ + function isArrayLike(value) { + return value != null && isLength(value.length) && !isFunction(value); + } + + /** + * This method is like `_.isArrayLike` except that it also checks if `value` + * is an object. + * + * @static + * @memberOf _ + * @since 4.0.0 + * @category Lang + * @param {*} value The value to check. + * @returns {boolean} Returns `true` if `value` is an array-like object, + * else `false`. + * @example + * + * _.isArrayLikeObject([1, 2, 3]); + * // => true + * + * _.isArrayLikeObject(document.body.children); + * // => true + * + * _.isArrayLikeObject('abc'); + * // => false + * + * _.isArrayLikeObject(_.noop); + * // => false + */ + function isArrayLikeObject(value) { + return isObjectLike(value) && isArrayLike(value); + } + + /** + * Checks if `value` is classified as a boolean primitive or object. + * + * @static + * @memberOf _ + * @since 0.1.0 + * @category Lang + * @param {*} value The value to check. + * @returns {boolean} Returns `true` if `value` is a boolean, else `false`. + * @example + * + * _.isBoolean(false); + * // => true + * + * _.isBoolean(null); + * // => false + */ + function isBoolean(value) { + return value === true || value === false || + (isObjectLike(value) && baseGetTag(value) == boolTag); + } + + /** + * Checks if `value` is a buffer. + * + * @static + * @memberOf _ + * @since 4.3.0 + * @category Lang + * @param {*} value The value to check. + * @returns {boolean} Returns `true` if `value` is a buffer, else `false`. + * @example + * + * _.isBuffer(new Buffer(2)); + * // => true + * + * _.isBuffer(new Uint8Array(2)); + * // => false + */ + var isBuffer = nativeIsBuffer || stubFalse; + + /** + * Checks if `value` is classified as a `Date` object. + * + * @static + * @memberOf _ + * @since 0.1.0 + * @category Lang + * @param {*} value The value to check. + * @returns {boolean} Returns `true` if `value` is a date object, else `false`. + * @example + * + * _.isDate(new Date); + * // => true + * + * _.isDate('Mon April 23 2012'); + * // => false + */ + var isDate = nodeIsDate ? baseUnary(nodeIsDate) : baseIsDate; + + /** + * Checks if `value` is likely a DOM element. + * + * @static + * @memberOf _ + * @since 0.1.0 + * @category Lang + * @param {*} value The value to check. + * @returns {boolean} Returns `true` if `value` is a DOM element, else `false`. + * @example + * + * _.isElement(document.body); + * // => true + * + * _.isElement(''); + * // => false + */ + function isElement(value) { + return isObjectLike(value) && value.nodeType === 1 && !isPlainObject(value); + } + + /** + * Checks if `value` is an empty object, collection, map, or set. + * + * Objects are considered empty if they have no own enumerable string keyed + * properties. + * + * Array-like values such as `arguments` objects, arrays, buffers, strings, or + * jQuery-like collections are considered empty if they have a `length` of `0`. + * Similarly, maps and sets are considered empty if they have a `size` of `0`. + * + * @static + * @memberOf _ + * @since 0.1.0 + * @category Lang + * @param {*} value The value to check. + * @returns {boolean} Returns `true` if `value` is empty, else `false`. + * @example + * + * _.isEmpty(null); + * // => true + * + * _.isEmpty(true); + * // => true + * + * _.isEmpty(1); + * // => true + * + * _.isEmpty([1, 2, 3]); + * // => false + * + * _.isEmpty({ 'a': 1 }); + * // => false + */ + function isEmpty(value) { + if (value == null) { + return true; + } + if (isArrayLike(value) && + (isArray(value) || typeof value == 'string' || typeof value.splice == 'function' || + isBuffer(value) || isTypedArray(value) || isArguments(value))) { + return !value.length; + } + var tag = getTag(value); + if (tag == mapTag || tag == setTag) { + return !value.size; + } + if (isPrototype(value)) { + return !baseKeys(value).length; + } + for (var key in value) { + if (hasOwnProperty.call(value, key)) { + return false; + } + } + return true; + } + + /** + * Performs a deep comparison between two values to determine if they are + * equivalent. + * + * **Note:** This method supports comparing arrays, array buffers, booleans, + * date objects, error objects, maps, numbers, `Object` objects, regexes, + * sets, strings, symbols, and typed arrays. `Object` objects are compared + * by their own, not inherited, enumerable properties. Functions and DOM + * nodes are compared by strict equality, i.e. `===`. + * + * @static + * @memberOf _ + * @since 0.1.0 + * @category Lang + * @param {*} value The value to compare. + * @param {*} other The other value to compare. + * @returns {boolean} Returns `true` if the values are equivalent, else `false`. + * @example + * + * var object = { 'a': 1 }; + * var other = { 'a': 1 }; + * + * _.isEqual(object, other); + * // => true + * + * object === other; + * // => false + */ + function isEqual(value, other) { + return baseIsEqual(value, other); + } + + /** + * This method is like `_.isEqual` except that it accepts `customizer` which + * is invoked to compare values. If `customizer` returns `undefined`, comparisons + * are handled by the method instead. The `customizer` is invoked with up to + * six arguments: (objValue, othValue [, index|key, object, other, stack]). + * + * @static + * @memberOf _ + * @since 4.0.0 + * @category Lang + * @param {*} value The value to compare. + * @param {*} other The other value to compare. + * @param {Function} [customizer] The function to customize comparisons. + * @returns {boolean} Returns `true` if the values are equivalent, else `false`. + * @example + * + * function isGreeting(value) { + * return /^h(?:i|ello)$/.test(value); + * } + * + * function customizer(objValue, othValue) { + * if (isGreeting(objValue) && isGreeting(othValue)) { + * return true; + * } + * } + * + * var array = ['hello', 'goodbye']; + * var other = ['hi', 'goodbye']; + * + * _.isEqualWith(array, other, customizer); + * // => true + */ + function isEqualWith(value, other, customizer) { + customizer = typeof customizer == 'function' ? customizer : undefined; + var result = customizer ? customizer(value, other) : undefined; + return result === undefined ? baseIsEqual(value, other, undefined, customizer) : !!result; + } + + /** + * Checks if `value` is an `Error`, `EvalError`, `RangeError`, `ReferenceError`, + * `SyntaxError`, `TypeError`, or `URIError` object. + * + * @static + * @memberOf _ + * @since 3.0.0 + * @category Lang + * @param {*} value The value to check. + * @returns {boolean} Returns `true` if `value` is an error object, else `false`. + * @example + * + * _.isError(new Error); + * // => true + * + * _.isError(Error); + * // => false + */ + function isError(value) { + if (!isObjectLike(value)) { + return false; + } + var tag = baseGetTag(value); + return tag == errorTag || tag == domExcTag || + (typeof value.message == 'string' && typeof value.name == 'string' && !isPlainObject(value)); + } + + /** + * Checks if `value` is a finite primitive number. + * + * **Note:** This method is based on + * [`Number.isFinite`](https://mdn.io/Number/isFinite). + * + * @static + * @memberOf _ + * @since 0.1.0 + * @category Lang + * @param {*} value The value to check. + * @returns {boolean} Returns `true` if `value` is a finite number, else `false`. + * @example + * + * _.isFinite(3); + * // => true + * + * _.isFinite(Number.MIN_VALUE); + * // => true + * + * _.isFinite(Infinity); + * // => false + * + * _.isFinite('3'); + * // => false + */ + function isFinite(value) { + return typeof value == 'number' && nativeIsFinite(value); + } + + /** + * Checks if `value` is classified as a `Function` object. + * + * @static + * @memberOf _ + * @since 0.1.0 + * @category Lang + * @param {*} value The value to check. + * @returns {boolean} Returns `true` if `value` is a function, else `false`. + * @example + * + * _.isFunction(_); + * // => true + * + * _.isFunction(/abc/); + * // => false + */ + function isFunction(value) { + if (!isObject(value)) { + return false; + } + // The use of `Object#toString` avoids issues with the `typeof` operator + // in Safari 9 which returns 'object' for typed arrays and other constructors. + var tag = baseGetTag(value); + return tag == funcTag || tag == genTag || tag == asyncTag || tag == proxyTag; + } + + /** + * Checks if `value` is an integer. + * + * **Note:** This method is based on + * [`Number.isInteger`](https://mdn.io/Number/isInteger). + * + * @static + * @memberOf _ + * @since 4.0.0 + * @category Lang + * @param {*} value The value to check. + * @returns {boolean} Returns `true` if `value` is an integer, else `false`. + * @example + * + * _.isInteger(3); + * // => true + * + * _.isInteger(Number.MIN_VALUE); + * // => false + * + * _.isInteger(Infinity); + * // => false + * + * _.isInteger('3'); + * // => false + */ + function isInteger(value) { + return typeof value == 'number' && value == toInteger(value); + } + + /** + * Checks if `value` is a valid array-like length. + * + * **Note:** This method is loosely based on + * [`ToLength`](http://ecma-international.org/ecma-262/7.0/#sec-tolength). + * + * @static + * @memberOf _ + * @since 4.0.0 + * @category Lang + * @param {*} value The value to check. + * @returns {boolean} Returns `true` if `value` is a valid length, else `false`. + * @example + * + * _.isLength(3); + * // => true + * + * _.isLength(Number.MIN_VALUE); + * // => false + * + * _.isLength(Infinity); + * // => false + * + * _.isLength('3'); + * // => false + */ + function isLength(value) { + return typeof value == 'number' && + value > -1 && value % 1 == 0 && value <= MAX_SAFE_INTEGER; + } + + /** + * Checks if `value` is the + * [language type](http://www.ecma-international.org/ecma-262/7.0/#sec-ecmascript-language-types) + * of `Object`. (e.g. arrays, functions, objects, regexes, `new Number(0)`, and `new String('')`) + * + * @static + * @memberOf _ + * @since 0.1.0 + * @category Lang + * @param {*} value The value to check. + * @returns {boolean} Returns `true` if `value` is an object, else `false`. + * @example + * + * _.isObject({}); + * // => true + * + * _.isObject([1, 2, 3]); + * // => true + * + * _.isObject(_.noop); + * // => true + * + * _.isObject(null); + * // => false + */ + function isObject(value) { + var type = typeof value; + return value != null && (type == 'object' || type == 'function'); + } + + /** + * Checks if `value` is object-like. A value is object-like if it's not `null` + * and has a `typeof` result of "object". + * + * @static + * @memberOf _ + * @since 4.0.0 + * @category Lang + * @param {*} value The value to check. + * @returns {boolean} Returns `true` if `value` is object-like, else `false`. + * @example + * + * _.isObjectLike({}); + * // => true + * + * _.isObjectLike([1, 2, 3]); + * // => true + * + * _.isObjectLike(_.noop); + * // => false + * + * _.isObjectLike(null); + * // => false + */ + function isObjectLike(value) { + return value != null && typeof value == 'object'; + } + + /** + * Checks if `value` is classified as a `Map` object. + * + * @static + * @memberOf _ + * @since 4.3.0 + * @category Lang + * @param {*} value The value to check. + * @returns {boolean} Returns `true` if `value` is a map, else `false`. + * @example + * + * _.isMap(new Map); + * // => true + * + * _.isMap(new WeakMap); + * // => false + */ + var isMap = nodeIsMap ? baseUnary(nodeIsMap) : baseIsMap; + + /** + * Performs a partial deep comparison between `object` and `source` to + * determine if `object` contains equivalent property values. + * + * **Note:** This method is equivalent to `_.matches` when `source` is + * partially applied. + * + * Partial comparisons will match empty array and empty object `source` + * values against any array or object value, respectively. See `_.isEqual` + * for a list of supported value comparisons. + * + * @static + * @memberOf _ + * @since 3.0.0 + * @category Lang + * @param {Object} object The object to inspect. + * @param {Object} source The object of property values to match. + * @returns {boolean} Returns `true` if `object` is a match, else `false`. + * @example + * + * var object = { 'a': 1, 'b': 2 }; + * + * _.isMatch(object, { 'b': 2 }); + * // => true + * + * _.isMatch(object, { 'b': 1 }); + * // => false + */ + function isMatch(object, source) { + return object === source || baseIsMatch(object, source, getMatchData(source)); + } + + /** + * This method is like `_.isMatch` except that it accepts `customizer` which + * is invoked to compare values. If `customizer` returns `undefined`, comparisons + * are handled by the method instead. The `customizer` is invoked with five + * arguments: (objValue, srcValue, index|key, object, source). + * + * @static + * @memberOf _ + * @since 4.0.0 + * @category Lang + * @param {Object} object The object to inspect. + * @param {Object} source The object of property values to match. + * @param {Function} [customizer] The function to customize comparisons. + * @returns {boolean} Returns `true` if `object` is a match, else `false`. + * @example + * + * function isGreeting(value) { + * return /^h(?:i|ello)$/.test(value); + * } + * + * function customizer(objValue, srcValue) { + * if (isGreeting(objValue) && isGreeting(srcValue)) { + * return true; + * } + * } + * + * var object = { 'greeting': 'hello' }; + * var source = { 'greeting': 'hi' }; + * + * _.isMatchWith(object, source, customizer); + * // => true + */ + function isMatchWith(object, source, customizer) { + customizer = typeof customizer == 'function' ? customizer : undefined; + return baseIsMatch(object, source, getMatchData(source), customizer); + } + + /** + * Checks if `value` is `NaN`. + * + * **Note:** This method is based on + * [`Number.isNaN`](https://mdn.io/Number/isNaN) and is not the same as + * global [`isNaN`](https://mdn.io/isNaN) which returns `true` for + * `undefined` and other non-number values. + * + * @static + * @memberOf _ + * @since 0.1.0 + * @category Lang + * @param {*} value The value to check. + * @returns {boolean} Returns `true` if `value` is `NaN`, else `false`. + * @example + * + * _.isNaN(NaN); + * // => true + * + * _.isNaN(new Number(NaN)); + * // => true + * + * isNaN(undefined); + * // => true + * + * _.isNaN(undefined); + * // => false + */ + function isNaN(value) { + // An `NaN` primitive is the only value that is not equal to itself. + // Perform the `toStringTag` check first to avoid errors with some + // ActiveX objects in IE. + return isNumber(value) && value != +value; + } + + /** + * Checks if `value` is a pristine native function. + * + * **Note:** This method can't reliably detect native functions in the presence + * of the core-js package because core-js circumvents this kind of detection. + * Despite multiple requests, the core-js maintainer has made it clear: any + * attempt to fix the detection will be obstructed. As a result, we're left + * with little choice but to throw an error. Unfortunately, this also affects + * packages, like [babel-polyfill](https://www.npmjs.com/package/babel-polyfill), + * which rely on core-js. + * + * @static + * @memberOf _ + * @since 3.0.0 + * @category Lang + * @param {*} value The value to check. + * @returns {boolean} Returns `true` if `value` is a native function, + * else `false`. + * @example + * + * _.isNative(Array.prototype.push); + * // => true + * + * _.isNative(_); + * // => false + */ + function isNative(value) { + if (isMaskable(value)) { + throw new Error(CORE_ERROR_TEXT); + } + return baseIsNative(value); + } + + /** + * Checks if `value` is `null`. + * + * @static + * @memberOf _ + * @since 0.1.0 + * @category Lang + * @param {*} value The value to check. + * @returns {boolean} Returns `true` if `value` is `null`, else `false`. + * @example + * + * _.isNull(null); + * // => true + * + * _.isNull(void 0); + * // => false + */ + function isNull(value) { + return value === null; + } + + /** + * Checks if `value` is `null` or `undefined`. + * + * @static + * @memberOf _ + * @since 4.0.0 + * @category Lang + * @param {*} value The value to check. + * @returns {boolean} Returns `true` if `value` is nullish, else `false`. + * @example + * + * _.isNil(null); + * // => true + * + * _.isNil(void 0); + * // => true + * + * _.isNil(NaN); + * // => false + */ + function isNil(value) { + return value == null; + } + + /** + * Checks if `value` is classified as a `Number` primitive or object. + * + * **Note:** To exclude `Infinity`, `-Infinity`, and `NaN`, which are + * classified as numbers, use the `_.isFinite` method. + * + * @static + * @memberOf _ + * @since 0.1.0 + * @category Lang + * @param {*} value The value to check. + * @returns {boolean} Returns `true` if `value` is a number, else `false`. + * @example + * + * _.isNumber(3); + * // => true + * + * _.isNumber(Number.MIN_VALUE); + * // => true + * + * _.isNumber(Infinity); + * // => true + * + * _.isNumber('3'); + * // => false + */ + function isNumber(value) { + return typeof value == 'number' || + (isObjectLike(value) && baseGetTag(value) == numberTag); + } + + /** + * Checks if `value` is a plain object, that is, an object created by the + * `Object` constructor or one with a `[[Prototype]]` of `null`. + * + * @static + * @memberOf _ + * @since 0.8.0 + * @category Lang + * @param {*} value The value to check. + * @returns {boolean} Returns `true` if `value` is a plain object, else `false`. + * @example + * + * function Foo() { + * this.a = 1; + * } + * + * _.isPlainObject(new Foo); + * // => false + * + * _.isPlainObject([1, 2, 3]); + * // => false + * + * _.isPlainObject({ 'x': 0, 'y': 0 }); + * // => true + * + * _.isPlainObject(Object.create(null)); + * // => true + */ + function isPlainObject(value) { + if (!isObjectLike(value) || baseGetTag(value) != objectTag) { + return false; + } + var proto = getPrototype(value); + if (proto === null) { + return true; + } + var Ctor = hasOwnProperty.call(proto, 'constructor') && proto.constructor; + return typeof Ctor == 'function' && Ctor instanceof Ctor && + funcToString.call(Ctor) == objectCtorString; + } + + /** + * Checks if `value` is classified as a `RegExp` object. + * + * @static + * @memberOf _ + * @since 0.1.0 + * @category Lang + * @param {*} value The value to check. + * @returns {boolean} Returns `true` if `value` is a regexp, else `false`. + * @example + * + * _.isRegExp(/abc/); + * // => true + * + * _.isRegExp('/abc/'); + * // => false + */ + var isRegExp = nodeIsRegExp ? baseUnary(nodeIsRegExp) : baseIsRegExp; + + /** + * Checks if `value` is a safe integer. An integer is safe if it's an IEEE-754 + * double precision number which isn't the result of a rounded unsafe integer. + * + * **Note:** This method is based on + * [`Number.isSafeInteger`](https://mdn.io/Number/isSafeInteger). + * + * @static + * @memberOf _ + * @since 4.0.0 + * @category Lang + * @param {*} value The value to check. + * @returns {boolean} Returns `true` if `value` is a safe integer, else `false`. + * @example + * + * _.isSafeInteger(3); + * // => true + * + * _.isSafeInteger(Number.MIN_VALUE); + * // => false + * + * _.isSafeInteger(Infinity); + * // => false + * + * _.isSafeInteger('3'); + * // => false + */ + function isSafeInteger(value) { + return isInteger(value) && value >= -MAX_SAFE_INTEGER && value <= MAX_SAFE_INTEGER; + } + + /** + * Checks if `value` is classified as a `Set` object. + * + * @static + * @memberOf _ + * @since 4.3.0 + * @category Lang + * @param {*} value The value to check. + * @returns {boolean} Returns `true` if `value` is a set, else `false`. + * @example + * + * _.isSet(new Set); + * // => true + * + * _.isSet(new WeakSet); + * // => false + */ + var isSet = nodeIsSet ? baseUnary(nodeIsSet) : baseIsSet; + + /** + * Checks if `value` is classified as a `String` primitive or object. + * + * @static + * @since 0.1.0 + * @memberOf _ + * @category Lang + * @param {*} value The value to check. + * @returns {boolean} Returns `true` if `value` is a string, else `false`. + * @example + * + * _.isString('abc'); + * // => true + * + * _.isString(1); + * // => false + */ + function isString(value) { + return typeof value == 'string' || + (!isArray(value) && isObjectLike(value) && baseGetTag(value) == stringTag); + } + + /** + * Checks if `value` is classified as a `Symbol` primitive or object. + * + * @static + * @memberOf _ + * @since 4.0.0 + * @category Lang + * @param {*} value The value to check. + * @returns {boolean} Returns `true` if `value` is a symbol, else `false`. + * @example + * + * _.isSymbol(Symbol.iterator); + * // => true + * + * _.isSymbol('abc'); + * // => false + */ + function isSymbol(value) { + return typeof value == 'symbol' || + (isObjectLike(value) && baseGetTag(value) == symbolTag); + } + + /** + * Checks if `value` is classified as a typed array. + * + * @static + * @memberOf _ + * @since 3.0.0 + * @category Lang + * @param {*} value The value to check. + * @returns {boolean} Returns `true` if `value` is a typed array, else `false`. + * @example + * + * _.isTypedArray(new Uint8Array); + * // => true + * + * _.isTypedArray([]); + * // => false + */ + var isTypedArray = nodeIsTypedArray ? baseUnary(nodeIsTypedArray) : baseIsTypedArray; + + /** + * Checks if `value` is `undefined`. + * + * @static + * @since 0.1.0 + * @memberOf _ + * @category Lang + * @param {*} value The value to check. + * @returns {boolean} Returns `true` if `value` is `undefined`, else `false`. + * @example + * + * _.isUndefined(void 0); + * // => true + * + * _.isUndefined(null); + * // => false + */ + function isUndefined(value) { + return value === undefined; + } + + /** + * Checks if `value` is classified as a `WeakMap` object. + * + * @static + * @memberOf _ + * @since 4.3.0 + * @category Lang + * @param {*} value The value to check. + * @returns {boolean} Returns `true` if `value` is a weak map, else `false`. + * @example + * + * _.isWeakMap(new WeakMap); + * // => true + * + * _.isWeakMap(new Map); + * // => false + */ + function isWeakMap(value) { + return isObjectLike(value) && getTag(value) == weakMapTag; + } + + /** + * Checks if `value` is classified as a `WeakSet` object. + * + * @static + * @memberOf _ + * @since 4.3.0 + * @category Lang + * @param {*} value The value to check. + * @returns {boolean} Returns `true` if `value` is a weak set, else `false`. + * @example + * + * _.isWeakSet(new WeakSet); + * // => true + * + * _.isWeakSet(new Set); + * // => false + */ + function isWeakSet(value) { + return isObjectLike(value) && baseGetTag(value) == weakSetTag; + } + + /** + * Checks if `value` is less than `other`. + * + * @static + * @memberOf _ + * @since 3.9.0 + * @category Lang + * @param {*} value The value to compare. + * @param {*} other The other value to compare. + * @returns {boolean} Returns `true` if `value` is less than `other`, + * else `false`. + * @see _.gt + * @example + * + * _.lt(1, 3); + * // => true + * + * _.lt(3, 3); + * // => false + * + * _.lt(3, 1); + * // => false + */ + var lt = createRelationalOperation(baseLt); + + /** + * Checks if `value` is less than or equal to `other`. + * + * @static + * @memberOf _ + * @since 3.9.0 + * @category Lang + * @param {*} value The value to compare. + * @param {*} other The other value to compare. + * @returns {boolean} Returns `true` if `value` is less than or equal to + * `other`, else `false`. + * @see _.gte + * @example + * + * _.lte(1, 3); + * // => true + * + * _.lte(3, 3); + * // => true + * + * _.lte(3, 1); + * // => false + */ + var lte = createRelationalOperation(function(value, other) { + return value <= other; + }); + + /** + * Converts `value` to an array. + * + * @static + * @since 0.1.0 + * @memberOf _ + * @category Lang + * @param {*} value The value to convert. + * @returns {Array} Returns the converted array. + * @example + * + * _.toArray({ 'a': 1, 'b': 2 }); + * // => [1, 2] + * + * _.toArray('abc'); + * // => ['a', 'b', 'c'] + * + * _.toArray(1); + * // => [] + * + * _.toArray(null); + * // => [] + */ + function toArray(value) { + if (!value) { + return []; + } + if (isArrayLike(value)) { + return isString(value) ? stringToArray(value) : copyArray(value); + } + if (symIterator && value[symIterator]) { + return iteratorToArray(value[symIterator]()); + } + var tag = getTag(value), + func = tag == mapTag ? mapToArray : (tag == setTag ? setToArray : values); + + return func(value); + } + + /** + * Converts `value` to a finite number. + * + * @static + * @memberOf _ + * @since 4.12.0 + * @category Lang + * @param {*} value The value to convert. + * @returns {number} Returns the converted number. + * @example + * + * _.toFinite(3.2); + * // => 3.2 + * + * _.toFinite(Number.MIN_VALUE); + * // => 5e-324 + * + * _.toFinite(Infinity); + * // => 1.7976931348623157e+308 + * + * _.toFinite('3.2'); + * // => 3.2 + */ + function toFinite(value) { + if (!value) { + return value === 0 ? value : 0; + } + value = toNumber(value); + if (value === INFINITY || value === -INFINITY) { + var sign = (value < 0 ? -1 : 1); + return sign * MAX_INTEGER; + } + return value === value ? value : 0; + } + + /** + * Converts `value` to an integer. + * + * **Note:** This method is loosely based on + * [`ToInteger`](http://www.ecma-international.org/ecma-262/7.0/#sec-tointeger). + * + * @static + * @memberOf _ + * @since 4.0.0 + * @category Lang + * @param {*} value The value to convert. + * @returns {number} Returns the converted integer. + * @example + * + * _.toInteger(3.2); + * // => 3 + * + * _.toInteger(Number.MIN_VALUE); + * // => 0 + * + * _.toInteger(Infinity); + * // => 1.7976931348623157e+308 + * + * _.toInteger('3.2'); + * // => 3 + */ + function toInteger(value) { + var result = toFinite(value), + remainder = result % 1; + + return result === result ? (remainder ? result - remainder : result) : 0; + } + + /** + * Converts `value` to an integer suitable for use as the length of an + * array-like object. + * + * **Note:** This method is based on + * [`ToLength`](http://ecma-international.org/ecma-262/7.0/#sec-tolength). + * + * @static + * @memberOf _ + * @since 4.0.0 + * @category Lang + * @param {*} value The value to convert. + * @returns {number} Returns the converted integer. + * @example + * + * _.toLength(3.2); + * // => 3 + * + * _.toLength(Number.MIN_VALUE); + * // => 0 + * + * _.toLength(Infinity); + * // => 4294967295 + * + * _.toLength('3.2'); + * // => 3 + */ + function toLength(value) { + return value ? baseClamp(toInteger(value), 0, MAX_ARRAY_LENGTH) : 0; + } + + /** + * Converts `value` to a number. + * + * @static + * @memberOf _ + * @since 4.0.0 + * @category Lang + * @param {*} value The value to process. + * @returns {number} Returns the number. + * @example + * + * _.toNumber(3.2); + * // => 3.2 + * + * _.toNumber(Number.MIN_VALUE); + * // => 5e-324 + * + * _.toNumber(Infinity); + * // => Infinity + * + * _.toNumber('3.2'); + * // => 3.2 + */ + function toNumber(value) { + if (typeof value == 'number') { + return value; + } + if (isSymbol(value)) { + return NAN; + } + if (isObject(value)) { + var other = typeof value.valueOf == 'function' ? value.valueOf() : value; + value = isObject(other) ? (other + '') : other; + } + if (typeof value != 'string') { + return value === 0 ? value : +value; + } + value = baseTrim(value); + var isBinary = reIsBinary.test(value); + return (isBinary || reIsOctal.test(value)) + ? freeParseInt(value.slice(2), isBinary ? 2 : 8) + : (reIsBadHex.test(value) ? NAN : +value); + } + + /** + * Converts `value` to a plain object flattening inherited enumerable string + * keyed properties of `value` to own properties of the plain object. + * + * @static + * @memberOf _ + * @since 3.0.0 + * @category Lang + * @param {*} value The value to convert. + * @returns {Object} Returns the converted plain object. + * @example + * + * function Foo() { + * this.b = 2; + * } + * + * Foo.prototype.c = 3; + * + * _.assign({ 'a': 1 }, new Foo); + * // => { 'a': 1, 'b': 2 } + * + * _.assign({ 'a': 1 }, _.toPlainObject(new Foo)); + * // => { 'a': 1, 'b': 2, 'c': 3 } + */ + function toPlainObject(value) { + return copyObject(value, keysIn(value)); + } + + /** + * Converts `value` to a safe integer. A safe integer can be compared and + * represented correctly. + * + * @static + * @memberOf _ + * @since 4.0.0 + * @category Lang + * @param {*} value The value to convert. + * @returns {number} Returns the converted integer. + * @example + * + * _.toSafeInteger(3.2); + * // => 3 + * + * _.toSafeInteger(Number.MIN_VALUE); + * // => 0 + * + * _.toSafeInteger(Infinity); + * // => 9007199254740991 + * + * _.toSafeInteger('3.2'); + * // => 3 + */ + function toSafeInteger(value) { + return value + ? baseClamp(toInteger(value), -MAX_SAFE_INTEGER, MAX_SAFE_INTEGER) + : (value === 0 ? value : 0); + } + + /** + * Converts `value` to a string. An empty string is returned for `null` + * and `undefined` values. The sign of `-0` is preserved. + * + * @static + * @memberOf _ + * @since 4.0.0 + * @category Lang + * @param {*} value The value to convert. + * @returns {string} Returns the converted string. + * @example + * + * _.toString(null); + * // => '' + * + * _.toString(-0); + * // => '-0' + * + * _.toString([1, 2, 3]); + * // => '1,2,3' + */ + function toString(value) { + return value == null ? '' : baseToString(value); + } + + /*------------------------------------------------------------------------*/ + + /** + * Assigns own enumerable string keyed properties of source objects to the + * destination object. Source objects are applied from left to right. + * Subsequent sources overwrite property assignments of previous sources. + * + * **Note:** This method mutates `object` and is loosely based on + * [`Object.assign`](https://mdn.io/Object/assign). + * + * @static + * @memberOf _ + * @since 0.10.0 + * @category Object + * @param {Object} object The destination object. + * @param {...Object} [sources] The source objects. + * @returns {Object} Returns `object`. + * @see _.assignIn + * @example + * + * function Foo() { + * this.a = 1; + * } + * + * function Bar() { + * this.c = 3; + * } + * + * Foo.prototype.b = 2; + * Bar.prototype.d = 4; + * + * _.assign({ 'a': 0 }, new Foo, new Bar); + * // => { 'a': 1, 'c': 3 } + */ + var assign = createAssigner(function(object, source) { + if (isPrototype(source) || isArrayLike(source)) { + copyObject(source, keys(source), object); + return; + } + for (var key in source) { + if (hasOwnProperty.call(source, key)) { + assignValue(object, key, source[key]); + } + } + }); + + /** + * This method is like `_.assign` except that it iterates over own and + * inherited source properties. + * + * **Note:** This method mutates `object`. + * + * @static + * @memberOf _ + * @since 4.0.0 + * @alias extend + * @category Object + * @param {Object} object The destination object. + * @param {...Object} [sources] The source objects. + * @returns {Object} Returns `object`. + * @see _.assign + * @example + * + * function Foo() { + * this.a = 1; + * } + * + * function Bar() { + * this.c = 3; + * } + * + * Foo.prototype.b = 2; + * Bar.prototype.d = 4; + * + * _.assignIn({ 'a': 0 }, new Foo, new Bar); + * // => { 'a': 1, 'b': 2, 'c': 3, 'd': 4 } + */ + var assignIn = createAssigner(function(object, source) { + copyObject(source, keysIn(source), object); + }); + + /** + * This method is like `_.assignIn` except that it accepts `customizer` + * which is invoked to produce the assigned values. If `customizer` returns + * `undefined`, assignment is handled by the method instead. The `customizer` + * is invoked with five arguments: (objValue, srcValue, key, object, source). + * + * **Note:** This method mutates `object`. + * + * @static + * @memberOf _ + * @since 4.0.0 + * @alias extendWith + * @category Object + * @param {Object} object The destination object. + * @param {...Object} sources The source objects. + * @param {Function} [customizer] The function to customize assigned values. + * @returns {Object} Returns `object`. + * @see _.assignWith + * @example + * + * function customizer(objValue, srcValue) { + * return _.isUndefined(objValue) ? srcValue : objValue; + * } + * + * var defaults = _.partialRight(_.assignInWith, customizer); + * + * defaults({ 'a': 1 }, { 'b': 2 }, { 'a': 3 }); + * // => { 'a': 1, 'b': 2 } + */ + var assignInWith = createAssigner(function(object, source, srcIndex, customizer) { + copyObject(source, keysIn(source), object, customizer); + }); + + /** + * This method is like `_.assign` except that it accepts `customizer` + * which is invoked to produce the assigned values. If `customizer` returns + * `undefined`, assignment is handled by the method instead. The `customizer` + * is invoked with five arguments: (objValue, srcValue, key, object, source). + * + * **Note:** This method mutates `object`. + * + * @static + * @memberOf _ + * @since 4.0.0 + * @category Object + * @param {Object} object The destination object. + * @param {...Object} sources The source objects. + * @param {Function} [customizer] The function to customize assigned values. + * @returns {Object} Returns `object`. + * @see _.assignInWith + * @example + * + * function customizer(objValue, srcValue) { + * return _.isUndefined(objValue) ? srcValue : objValue; + * } + * + * var defaults = _.partialRight(_.assignWith, customizer); + * + * defaults({ 'a': 1 }, { 'b': 2 }, { 'a': 3 }); + * // => { 'a': 1, 'b': 2 } + */ + var assignWith = createAssigner(function(object, source, srcIndex, customizer) { + copyObject(source, keys(source), object, customizer); + }); + + /** + * Creates an array of values corresponding to `paths` of `object`. + * + * @static + * @memberOf _ + * @since 1.0.0 + * @category Object + * @param {Object} object The object to iterate over. + * @param {...(string|string[])} [paths] The property paths to pick. + * @returns {Array} Returns the picked values. + * @example + * + * var object = { 'a': [{ 'b': { 'c': 3 } }, 4] }; + * + * _.at(object, ['a[0].b.c', 'a[1]']); + * // => [3, 4] + */ + var at = flatRest(baseAt); + + /** + * Creates an object that inherits from the `prototype` object. If a + * `properties` object is given, its own enumerable string keyed properties + * are assigned to the created object. + * + * @static + * @memberOf _ + * @since 2.3.0 + * @category Object + * @param {Object} prototype The object to inherit from. + * @param {Object} [properties] The properties to assign to the object. + * @returns {Object} Returns the new object. + * @example + * + * function Shape() { + * this.x = 0; + * this.y = 0; + * } + * + * function Circle() { + * Shape.call(this); + * } + * + * Circle.prototype = _.create(Shape.prototype, { + * 'constructor': Circle + * }); + * + * var circle = new Circle; + * circle instanceof Circle; + * // => true + * + * circle instanceof Shape; + * // => true + */ + function create(prototype, properties) { + var result = baseCreate(prototype); + return properties == null ? result : baseAssign(result, properties); + } + + /** + * Assigns own and inherited enumerable string keyed properties of source + * objects to the destination object for all destination properties that + * resolve to `undefined`. Source objects are applied from left to right. + * Once a property is set, additional values of the same property are ignored. + * + * **Note:** This method mutates `object`. + * + * @static + * @since 0.1.0 + * @memberOf _ + * @category Object + * @param {Object} object The destination object. + * @param {...Object} [sources] The source objects. + * @returns {Object} Returns `object`. + * @see _.defaultsDeep + * @example + * + * _.defaults({ 'a': 1 }, { 'b': 2 }, { 'a': 3 }); + * // => { 'a': 1, 'b': 2 } + */ + var defaults = baseRest(function(object, sources) { + object = Object(object); + + var index = -1; + var length = sources.length; + var guard = length > 2 ? sources[2] : undefined; + + if (guard && isIterateeCall(sources[0], sources[1], guard)) { + length = 1; + } + + while (++index < length) { + var source = sources[index]; + var props = keysIn(source); + var propsIndex = -1; + var propsLength = props.length; + + while (++propsIndex < propsLength) { + var key = props[propsIndex]; + var value = object[key]; + + if (value === undefined || + (eq(value, objectProto[key]) && !hasOwnProperty.call(object, key))) { + object[key] = source[key]; + } + } + } + + return object; + }); + + /** + * This method is like `_.defaults` except that it recursively assigns + * default properties. + * + * **Note:** This method mutates `object`. + * + * @static + * @memberOf _ + * @since 3.10.0 + * @category Object + * @param {Object} object The destination object. + * @param {...Object} [sources] The source objects. + * @returns {Object} Returns `object`. + * @see _.defaults + * @example + * + * _.defaultsDeep({ 'a': { 'b': 2 } }, { 'a': { 'b': 1, 'c': 3 } }); + * // => { 'a': { 'b': 2, 'c': 3 } } + */ + var defaultsDeep = baseRest(function(args) { + args.push(undefined, customDefaultsMerge); + return apply(mergeWith, undefined, args); + }); + + /** + * This method is like `_.find` except that it returns the key of the first + * element `predicate` returns truthy for instead of the element itself. + * + * @static + * @memberOf _ + * @since 1.1.0 + * @category Object + * @param {Object} object The object to inspect. + * @param {Function} [predicate=_.identity] The function invoked per iteration. + * @returns {string|undefined} Returns the key of the matched element, + * else `undefined`. + * @example + * + * var users = { + * 'barney': { 'age': 36, 'active': true }, + * 'fred': { 'age': 40, 'active': false }, + * 'pebbles': { 'age': 1, 'active': true } + * }; + * + * _.findKey(users, function(o) { return o.age < 40; }); + * // => 'barney' (iteration order is not guaranteed) + * + * // The `_.matches` iteratee shorthand. + * _.findKey(users, { 'age': 1, 'active': true }); + * // => 'pebbles' + * + * // The `_.matchesProperty` iteratee shorthand. + * _.findKey(users, ['active', false]); + * // => 'fred' + * + * // The `_.property` iteratee shorthand. + * _.findKey(users, 'active'); + * // => 'barney' + */ + function findKey(object, predicate) { + return baseFindKey(object, getIteratee(predicate, 3), baseForOwn); + } + + /** + * This method is like `_.findKey` except that it iterates over elements of + * a collection in the opposite order. + * + * @static + * @memberOf _ + * @since 2.0.0 + * @category Object + * @param {Object} object The object to inspect. + * @param {Function} [predicate=_.identity] The function invoked per iteration. + * @returns {string|undefined} Returns the key of the matched element, + * else `undefined`. + * @example + * + * var users = { + * 'barney': { 'age': 36, 'active': true }, + * 'fred': { 'age': 40, 'active': false }, + * 'pebbles': { 'age': 1, 'active': true } + * }; + * + * _.findLastKey(users, function(o) { return o.age < 40; }); + * // => returns 'pebbles' assuming `_.findKey` returns 'barney' + * + * // The `_.matches` iteratee shorthand. + * _.findLastKey(users, { 'age': 36, 'active': true }); + * // => 'barney' + * + * // The `_.matchesProperty` iteratee shorthand. + * _.findLastKey(users, ['active', false]); + * // => 'fred' + * + * // The `_.property` iteratee shorthand. + * _.findLastKey(users, 'active'); + * // => 'pebbles' + */ + function findLastKey(object, predicate) { + return baseFindKey(object, getIteratee(predicate, 3), baseForOwnRight); + } + + /** + * Iterates over own and inherited enumerable string keyed properties of an + * object and invokes `iteratee` for each property. The iteratee is invoked + * with three arguments: (value, key, object). Iteratee functions may exit + * iteration early by explicitly returning `false`. + * + * @static + * @memberOf _ + * @since 0.3.0 + * @category Object + * @param {Object} object The object to iterate over. + * @param {Function} [iteratee=_.identity] The function invoked per iteration. + * @returns {Object} Returns `object`. + * @see _.forInRight + * @example + * + * function Foo() { + * this.a = 1; + * this.b = 2; + * } + * + * Foo.prototype.c = 3; + * + * _.forIn(new Foo, function(value, key) { + * console.log(key); + * }); + * // => Logs 'a', 'b', then 'c' (iteration order is not guaranteed). + */ + function forIn(object, iteratee) { + return object == null + ? object + : baseFor(object, getIteratee(iteratee, 3), keysIn); + } + + /** + * This method is like `_.forIn` except that it iterates over properties of + * `object` in the opposite order. + * + * @static + * @memberOf _ + * @since 2.0.0 + * @category Object + * @param {Object} object The object to iterate over. + * @param {Function} [iteratee=_.identity] The function invoked per iteration. + * @returns {Object} Returns `object`. + * @see _.forIn + * @example + * + * function Foo() { + * this.a = 1; + * this.b = 2; + * } + * + * Foo.prototype.c = 3; + * + * _.forInRight(new Foo, function(value, key) { + * console.log(key); + * }); + * // => Logs 'c', 'b', then 'a' assuming `_.forIn` logs 'a', 'b', then 'c'. + */ + function forInRight(object, iteratee) { + return object == null + ? object + : baseForRight(object, getIteratee(iteratee, 3), keysIn); + } + + /** + * Iterates over own enumerable string keyed properties of an object and + * invokes `iteratee` for each property. The iteratee is invoked with three + * arguments: (value, key, object). Iteratee functions may exit iteration + * early by explicitly returning `false`. + * + * @static + * @memberOf _ + * @since 0.3.0 + * @category Object + * @param {Object} object The object to iterate over. + * @param {Function} [iteratee=_.identity] The function invoked per iteration. + * @returns {Object} Returns `object`. + * @see _.forOwnRight + * @example + * + * function Foo() { + * this.a = 1; + * this.b = 2; + * } + * + * Foo.prototype.c = 3; + * + * _.forOwn(new Foo, function(value, key) { + * console.log(key); + * }); + * // => Logs 'a' then 'b' (iteration order is not guaranteed). + */ + function forOwn(object, iteratee) { + return object && baseForOwn(object, getIteratee(iteratee, 3)); + } + + /** + * This method is like `_.forOwn` except that it iterates over properties of + * `object` in the opposite order. + * + * @static + * @memberOf _ + * @since 2.0.0 + * @category Object + * @param {Object} object The object to iterate over. + * @param {Function} [iteratee=_.identity] The function invoked per iteration. + * @returns {Object} Returns `object`. + * @see _.forOwn + * @example + * + * function Foo() { + * this.a = 1; + * this.b = 2; + * } + * + * Foo.prototype.c = 3; + * + * _.forOwnRight(new Foo, function(value, key) { + * console.log(key); + * }); + * // => Logs 'b' then 'a' assuming `_.forOwn` logs 'a' then 'b'. + */ + function forOwnRight(object, iteratee) { + return object && baseForOwnRight(object, getIteratee(iteratee, 3)); + } + + /** + * Creates an array of function property names from own enumerable properties + * of `object`. + * + * @static + * @since 0.1.0 + * @memberOf _ + * @category Object + * @param {Object} object The object to inspect. + * @returns {Array} Returns the function names. + * @see _.functionsIn + * @example + * + * function Foo() { + * this.a = _.constant('a'); + * this.b = _.constant('b'); + * } + * + * Foo.prototype.c = _.constant('c'); + * + * _.functions(new Foo); + * // => ['a', 'b'] + */ + function functions(object) { + return object == null ? [] : baseFunctions(object, keys(object)); + } + + /** + * Creates an array of function property names from own and inherited + * enumerable properties of `object`. + * + * @static + * @memberOf _ + * @since 4.0.0 + * @category Object + * @param {Object} object The object to inspect. + * @returns {Array} Returns the function names. + * @see _.functions + * @example + * + * function Foo() { + * this.a = _.constant('a'); + * this.b = _.constant('b'); + * } + * + * Foo.prototype.c = _.constant('c'); + * + * _.functionsIn(new Foo); + * // => ['a', 'b', 'c'] + */ + function functionsIn(object) { + return object == null ? [] : baseFunctions(object, keysIn(object)); + } + + /** + * Gets the value at `path` of `object`. If the resolved value is + * `undefined`, the `defaultValue` is returned in its place. + * + * @static + * @memberOf _ + * @since 3.7.0 + * @category Object + * @param {Object} object The object to query. + * @param {Array|string} path The path of the property to get. + * @param {*} [defaultValue] The value returned for `undefined` resolved values. + * @returns {*} Returns the resolved value. + * @example + * + * var object = { 'a': [{ 'b': { 'c': 3 } }] }; + * + * _.get(object, 'a[0].b.c'); + * // => 3 + * + * _.get(object, ['a', '0', 'b', 'c']); + * // => 3 + * + * _.get(object, 'a.b.c', 'default'); + * // => 'default' + */ + function get(object, path, defaultValue) { + var result = object == null ? undefined : baseGet(object, path); + return result === undefined ? defaultValue : result; + } + + /** + * Checks if `path` is a direct property of `object`. + * + * @static + * @since 0.1.0 + * @memberOf _ + * @category Object + * @param {Object} object The object to query. + * @param {Array|string} path The path to check. + * @returns {boolean} Returns `true` if `path` exists, else `false`. + * @example + * + * var object = { 'a': { 'b': 2 } }; + * var other = _.create({ 'a': _.create({ 'b': 2 }) }); + * + * _.has(object, 'a'); + * // => true + * + * _.has(object, 'a.b'); + * // => true + * + * _.has(object, ['a', 'b']); + * // => true + * + * _.has(other, 'a'); + * // => false + */ + function has(object, path) { + return object != null && hasPath(object, path, baseHas); + } + + /** + * Checks if `path` is a direct or inherited property of `object`. + * + * @static + * @memberOf _ + * @since 4.0.0 + * @category Object + * @param {Object} object The object to query. + * @param {Array|string} path The path to check. + * @returns {boolean} Returns `true` if `path` exists, else `false`. + * @example + * + * var object = _.create({ 'a': _.create({ 'b': 2 }) }); + * + * _.hasIn(object, 'a'); + * // => true + * + * _.hasIn(object, 'a.b'); + * // => true + * + * _.hasIn(object, ['a', 'b']); + * // => true + * + * _.hasIn(object, 'b'); + * // => false + */ + function hasIn(object, path) { + return object != null && hasPath(object, path, baseHasIn); + } + + /** + * Creates an object composed of the inverted keys and values of `object`. + * If `object` contains duplicate values, subsequent values overwrite + * property assignments of previous values. + * + * @static + * @memberOf _ + * @since 0.7.0 + * @category Object + * @param {Object} object The object to invert. + * @returns {Object} Returns the new inverted object. + * @example + * + * var object = { 'a': 1, 'b': 2, 'c': 1 }; + * + * _.invert(object); + * // => { '1': 'c', '2': 'b' } + */ + var invert = createInverter(function(result, value, key) { + if (value != null && + typeof value.toString != 'function') { + value = nativeObjectToString.call(value); + } + + result[value] = key; + }, constant(identity)); + + /** + * This method is like `_.invert` except that the inverted object is generated + * from the results of running each element of `object` thru `iteratee`. The + * corresponding inverted value of each inverted key is an array of keys + * responsible for generating the inverted value. The iteratee is invoked + * with one argument: (value). + * + * @static + * @memberOf _ + * @since 4.1.0 + * @category Object + * @param {Object} object The object to invert. + * @param {Function} [iteratee=_.identity] The iteratee invoked per element. + * @returns {Object} Returns the new inverted object. + * @example + * + * var object = { 'a': 1, 'b': 2, 'c': 1 }; + * + * _.invertBy(object); + * // => { '1': ['a', 'c'], '2': ['b'] } + * + * _.invertBy(object, function(value) { + * return 'group' + value; + * }); + * // => { 'group1': ['a', 'c'], 'group2': ['b'] } + */ + var invertBy = createInverter(function(result, value, key) { + if (value != null && + typeof value.toString != 'function') { + value = nativeObjectToString.call(value); + } + + if (hasOwnProperty.call(result, value)) { + result[value].push(key); + } else { + result[value] = [key]; + } + }, getIteratee); + + /** + * Invokes the method at `path` of `object`. + * + * @static + * @memberOf _ + * @since 4.0.0 + * @category Object + * @param {Object} object The object to query. + * @param {Array|string} path The path of the method to invoke. + * @param {...*} [args] The arguments to invoke the method with. + * @returns {*} Returns the result of the invoked method. + * @example + * + * var object = { 'a': [{ 'b': { 'c': [1, 2, 3, 4] } }] }; + * + * _.invoke(object, 'a[0].b.c.slice', 1, 3); + * // => [2, 3] + */ + var invoke = baseRest(baseInvoke); + + /** + * Creates an array of the own enumerable property names of `object`. + * + * **Note:** Non-object values are coerced to objects. See the + * [ES spec](http://ecma-international.org/ecma-262/7.0/#sec-object.keys) + * for more details. + * + * @static + * @since 0.1.0 + * @memberOf _ + * @category Object + * @param {Object} object The object to query. + * @returns {Array} Returns the array of property names. + * @example + * + * function Foo() { + * this.a = 1; + * this.b = 2; + * } + * + * Foo.prototype.c = 3; + * + * _.keys(new Foo); + * // => ['a', 'b'] (iteration order is not guaranteed) + * + * _.keys('hi'); + * // => ['0', '1'] + */ + function keys(object) { + return isArrayLike(object) ? arrayLikeKeys(object) : baseKeys(object); + } + + /** + * Creates an array of the own and inherited enumerable property names of `object`. + * + * **Note:** Non-object values are coerced to objects. + * + * @static + * @memberOf _ + * @since 3.0.0 + * @category Object + * @param {Object} object The object to query. + * @returns {Array} Returns the array of property names. + * @example + * + * function Foo() { + * this.a = 1; + * this.b = 2; + * } + * + * Foo.prototype.c = 3; + * + * _.keysIn(new Foo); + * // => ['a', 'b', 'c'] (iteration order is not guaranteed) + */ + function keysIn(object) { + return isArrayLike(object) ? arrayLikeKeys(object, true) : baseKeysIn(object); + } + + /** + * The opposite of `_.mapValues`; this method creates an object with the + * same values as `object` and keys generated by running each own enumerable + * string keyed property of `object` thru `iteratee`. The iteratee is invoked + * with three arguments: (value, key, object). + * + * @static + * @memberOf _ + * @since 3.8.0 + * @category Object + * @param {Object} object The object to iterate over. + * @param {Function} [iteratee=_.identity] The function invoked per iteration. + * @returns {Object} Returns the new mapped object. + * @see _.mapValues + * @example + * + * _.mapKeys({ 'a': 1, 'b': 2 }, function(value, key) { + * return key + value; + * }); + * // => { 'a1': 1, 'b2': 2 } + */ + function mapKeys(object, iteratee) { + var result = {}; + iteratee = getIteratee(iteratee, 3); + + baseForOwn(object, function(value, key, object) { + baseAssignValue(result, iteratee(value, key, object), value); + }); + return result; + } + + /** + * Creates an object with the same keys as `object` and values generated + * by running each own enumerable string keyed property of `object` thru + * `iteratee`. The iteratee is invoked with three arguments: + * (value, key, object). + * + * @static + * @memberOf _ + * @since 2.4.0 + * @category Object + * @param {Object} object The object to iterate over. + * @param {Function} [iteratee=_.identity] The function invoked per iteration. + * @returns {Object} Returns the new mapped object. + * @see _.mapKeys + * @example + * + * var users = { + * 'fred': { 'user': 'fred', 'age': 40 }, + * 'pebbles': { 'user': 'pebbles', 'age': 1 } + * }; + * + * _.mapValues(users, function(o) { return o.age; }); + * // => { 'fred': 40, 'pebbles': 1 } (iteration order is not guaranteed) + * + * // The `_.property` iteratee shorthand. + * _.mapValues(users, 'age'); + * // => { 'fred': 40, 'pebbles': 1 } (iteration order is not guaranteed) + */ + function mapValues(object, iteratee) { + var result = {}; + iteratee = getIteratee(iteratee, 3); + + baseForOwn(object, function(value, key, object) { + baseAssignValue(result, key, iteratee(value, key, object)); + }); + return result; + } + + /** + * This method is like `_.assign` except that it recursively merges own and + * inherited enumerable string keyed properties of source objects into the + * destination object. Source properties that resolve to `undefined` are + * skipped if a destination value exists. Array and plain object properties + * are merged recursively. Other objects and value types are overridden by + * assignment. Source objects are applied from left to right. Subsequent + * sources overwrite property assignments of previous sources. + * + * **Note:** This method mutates `object`. + * + * @static + * @memberOf _ + * @since 0.5.0 + * @category Object + * @param {Object} object The destination object. + * @param {...Object} [sources] The source objects. + * @returns {Object} Returns `object`. + * @example + * + * var object = { + * 'a': [{ 'b': 2 }, { 'd': 4 }] + * }; + * + * var other = { + * 'a': [{ 'c': 3 }, { 'e': 5 }] + * }; + * + * _.merge(object, other); + * // => { 'a': [{ 'b': 2, 'c': 3 }, { 'd': 4, 'e': 5 }] } + */ + var merge = createAssigner(function(object, source, srcIndex) { + baseMerge(object, source, srcIndex); + }); + + /** + * This method is like `_.merge` except that it accepts `customizer` which + * is invoked to produce the merged values of the destination and source + * properties. If `customizer` returns `undefined`, merging is handled by the + * method instead. The `customizer` is invoked with six arguments: + * (objValue, srcValue, key, object, source, stack). + * + * **Note:** This method mutates `object`. + * + * @static + * @memberOf _ + * @since 4.0.0 + * @category Object + * @param {Object} object The destination object. + * @param {...Object} sources The source objects. + * @param {Function} customizer The function to customize assigned values. + * @returns {Object} Returns `object`. + * @example + * + * function customizer(objValue, srcValue) { + * if (_.isArray(objValue)) { + * return objValue.concat(srcValue); + * } + * } + * + * var object = { 'a': [1], 'b': [2] }; + * var other = { 'a': [3], 'b': [4] }; + * + * _.mergeWith(object, other, customizer); + * // => { 'a': [1, 3], 'b': [2, 4] } + */ + var mergeWith = createAssigner(function(object, source, srcIndex, customizer) { + baseMerge(object, source, srcIndex, customizer); + }); + + /** + * The opposite of `_.pick`; this method creates an object composed of the + * own and inherited enumerable property paths of `object` that are not omitted. + * + * **Note:** This method is considerably slower than `_.pick`. + * + * @static + * @since 0.1.0 + * @memberOf _ + * @category Object + * @param {Object} object The source object. + * @param {...(string|string[])} [paths] The property paths to omit. + * @returns {Object} Returns the new object. + * @example + * + * var object = { 'a': 1, 'b': '2', 'c': 3 }; + * + * _.omit(object, ['a', 'c']); + * // => { 'b': '2' } + */ + var omit = flatRest(function(object, paths) { + var result = {}; + if (object == null) { + return result; + } + var isDeep = false; + paths = arrayMap(paths, function(path) { + path = castPath(path, object); + isDeep || (isDeep = path.length > 1); + return path; + }); + copyObject(object, getAllKeysIn(object), result); + if (isDeep) { + result = baseClone(result, CLONE_DEEP_FLAG | CLONE_FLAT_FLAG | CLONE_SYMBOLS_FLAG, customOmitClone); + } + var length = paths.length; + while (length--) { + baseUnset(result, paths[length]); + } + return result; + }); + + /** + * The opposite of `_.pickBy`; this method creates an object composed of + * the own and inherited enumerable string keyed properties of `object` that + * `predicate` doesn't return truthy for. The predicate is invoked with two + * arguments: (value, key). + * + * @static + * @memberOf _ + * @since 4.0.0 + * @category Object + * @param {Object} object The source object. + * @param {Function} [predicate=_.identity] The function invoked per property. + * @returns {Object} Returns the new object. + * @example + * + * var object = { 'a': 1, 'b': '2', 'c': 3 }; + * + * _.omitBy(object, _.isNumber); + * // => { 'b': '2' } + */ + function omitBy(object, predicate) { + return pickBy(object, negate(getIteratee(predicate))); + } + + /** + * Creates an object composed of the picked `object` properties. + * + * @static + * @since 0.1.0 + * @memberOf _ + * @category Object + * @param {Object} object The source object. + * @param {...(string|string[])} [paths] The property paths to pick. + * @returns {Object} Returns the new object. + * @example + * + * var object = { 'a': 1, 'b': '2', 'c': 3 }; + * + * _.pick(object, ['a', 'c']); + * // => { 'a': 1, 'c': 3 } + */ + var pick = flatRest(function(object, paths) { + return object == null ? {} : basePick(object, paths); + }); + + /** + * Creates an object composed of the `object` properties `predicate` returns + * truthy for. The predicate is invoked with two arguments: (value, key). + * + * @static + * @memberOf _ + * @since 4.0.0 + * @category Object + * @param {Object} object The source object. + * @param {Function} [predicate=_.identity] The function invoked per property. + * @returns {Object} Returns the new object. + * @example + * + * var object = { 'a': 1, 'b': '2', 'c': 3 }; + * + * _.pickBy(object, _.isNumber); + * // => { 'a': 1, 'c': 3 } + */ + function pickBy(object, predicate) { + if (object == null) { + return {}; + } + var props = arrayMap(getAllKeysIn(object), function(prop) { + return [prop]; + }); + predicate = getIteratee(predicate); + return basePickBy(object, props, function(value, path) { + return predicate(value, path[0]); + }); + } + + /** + * This method is like `_.get` except that if the resolved value is a + * function it's invoked with the `this` binding of its parent object and + * its result is returned. + * + * @static + * @since 0.1.0 + * @memberOf _ + * @category Object + * @param {Object} object The object to query. + * @param {Array|string} path The path of the property to resolve. + * @param {*} [defaultValue] The value returned for `undefined` resolved values. + * @returns {*} Returns the resolved value. + * @example + * + * var object = { 'a': [{ 'b': { 'c1': 3, 'c2': _.constant(4) } }] }; + * + * _.result(object, 'a[0].b.c1'); + * // => 3 + * + * _.result(object, 'a[0].b.c2'); + * // => 4 + * + * _.result(object, 'a[0].b.c3', 'default'); + * // => 'default' + * + * _.result(object, 'a[0].b.c3', _.constant('default')); + * // => 'default' + */ + function result(object, path, defaultValue) { + path = castPath(path, object); + + var index = -1, + length = path.length; + + // Ensure the loop is entered when path is empty. + if (!length) { + length = 1; + object = undefined; + } + while (++index < length) { + var value = object == null ? undefined : object[toKey(path[index])]; + if (value === undefined) { + index = length; + value = defaultValue; + } + object = isFunction(value) ? value.call(object) : value; + } + return object; + } + + /** + * Sets the value at `path` of `object`. If a portion of `path` doesn't exist, + * it's created. Arrays are created for missing index properties while objects + * are created for all other missing properties. Use `_.setWith` to customize + * `path` creation. + * + * **Note:** This method mutates `object`. + * + * @static + * @memberOf _ + * @since 3.7.0 + * @category Object + * @param {Object} object The object to modify. + * @param {Array|string} path The path of the property to set. + * @param {*} value The value to set. + * @returns {Object} Returns `object`. + * @example + * + * var object = { 'a': [{ 'b': { 'c': 3 } }] }; + * + * _.set(object, 'a[0].b.c', 4); + * console.log(object.a[0].b.c); + * // => 4 + * + * _.set(object, ['x', '0', 'y', 'z'], 5); + * console.log(object.x[0].y.z); + * // => 5 + */ + function set(object, path, value) { + return object == null ? object : baseSet(object, path, value); + } + + /** + * This method is like `_.set` except that it accepts `customizer` which is + * invoked to produce the objects of `path`. If `customizer` returns `undefined` + * path creation is handled by the method instead. The `customizer` is invoked + * with three arguments: (nsValue, key, nsObject). + * + * **Note:** This method mutates `object`. + * + * @static + * @memberOf _ + * @since 4.0.0 + * @category Object + * @param {Object} object The object to modify. + * @param {Array|string} path The path of the property to set. + * @param {*} value The value to set. + * @param {Function} [customizer] The function to customize assigned values. + * @returns {Object} Returns `object`. + * @example + * + * var object = {}; + * + * _.setWith(object, '[0][1]', 'a', Object); + * // => { '0': { '1': 'a' } } + */ + function setWith(object, path, value, customizer) { + customizer = typeof customizer == 'function' ? customizer : undefined; + return object == null ? object : baseSet(object, path, value, customizer); + } + + /** + * Creates an array of own enumerable string keyed-value pairs for `object` + * which can be consumed by `_.fromPairs`. If `object` is a map or set, its + * entries are returned. + * + * @static + * @memberOf _ + * @since 4.0.0 + * @alias entries + * @category Object + * @param {Object} object The object to query. + * @returns {Array} Returns the key-value pairs. + * @example + * + * function Foo() { + * this.a = 1; + * this.b = 2; + * } + * + * Foo.prototype.c = 3; + * + * _.toPairs(new Foo); + * // => [['a', 1], ['b', 2]] (iteration order is not guaranteed) + */ + var toPairs = createToPairs(keys); + + /** + * Creates an array of own and inherited enumerable string keyed-value pairs + * for `object` which can be consumed by `_.fromPairs`. If `object` is a map + * or set, its entries are returned. + * + * @static + * @memberOf _ + * @since 4.0.0 + * @alias entriesIn + * @category Object + * @param {Object} object The object to query. + * @returns {Array} Returns the key-value pairs. + * @example + * + * function Foo() { + * this.a = 1; + * this.b = 2; + * } + * + * Foo.prototype.c = 3; + * + * _.toPairsIn(new Foo); + * // => [['a', 1], ['b', 2], ['c', 3]] (iteration order is not guaranteed) + */ + var toPairsIn = createToPairs(keysIn); + + /** + * An alternative to `_.reduce`; this method transforms `object` to a new + * `accumulator` object which is the result of running each of its own + * enumerable string keyed properties thru `iteratee`, with each invocation + * potentially mutating the `accumulator` object. If `accumulator` is not + * provided, a new object with the same `[[Prototype]]` will be used. The + * iteratee is invoked with four arguments: (accumulator, value, key, object). + * Iteratee functions may exit iteration early by explicitly returning `false`. + * + * @static + * @memberOf _ + * @since 1.3.0 + * @category Object + * @param {Object} object The object to iterate over. + * @param {Function} [iteratee=_.identity] The function invoked per iteration. + * @param {*} [accumulator] The custom accumulator value. + * @returns {*} Returns the accumulated value. + * @example + * + * _.transform([2, 3, 4], function(result, n) { + * result.push(n *= n); + * return n % 2 == 0; + * }, []); + * // => [4, 9] + * + * _.transform({ 'a': 1, 'b': 2, 'c': 1 }, function(result, value, key) { + * (result[value] || (result[value] = [])).push(key); + * }, {}); + * // => { '1': ['a', 'c'], '2': ['b'] } + */ + function transform(object, iteratee, accumulator) { + var isArr = isArray(object), + isArrLike = isArr || isBuffer(object) || isTypedArray(object); + + iteratee = getIteratee(iteratee, 4); + if (accumulator == null) { + var Ctor = object && object.constructor; + if (isArrLike) { + accumulator = isArr ? new Ctor : []; + } + else if (isObject(object)) { + accumulator = isFunction(Ctor) ? baseCreate(getPrototype(object)) : {}; + } + else { + accumulator = {}; + } + } + (isArrLike ? arrayEach : baseForOwn)(object, function(value, index, object) { + return iteratee(accumulator, value, index, object); + }); + return accumulator; + } + + /** + * Removes the property at `path` of `object`. + * + * **Note:** This method mutates `object`. + * + * @static + * @memberOf _ + * @since 4.0.0 + * @category Object + * @param {Object} object The object to modify. + * @param {Array|string} path The path of the property to unset. + * @returns {boolean} Returns `true` if the property is deleted, else `false`. + * @example + * + * var object = { 'a': [{ 'b': { 'c': 7 } }] }; + * _.unset(object, 'a[0].b.c'); + * // => true + * + * console.log(object); + * // => { 'a': [{ 'b': {} }] }; + * + * _.unset(object, ['a', '0', 'b', 'c']); + * // => true + * + * console.log(object); + * // => { 'a': [{ 'b': {} }] }; + */ + function unset(object, path) { + return object == null ? true : baseUnset(object, path); + } + + /** + * This method is like `_.set` except that accepts `updater` to produce the + * value to set. Use `_.updateWith` to customize `path` creation. The `updater` + * is invoked with one argument: (value). + * + * **Note:** This method mutates `object`. + * + * @static + * @memberOf _ + * @since 4.6.0 + * @category Object + * @param {Object} object The object to modify. + * @param {Array|string} path The path of the property to set. + * @param {Function} updater The function to produce the updated value. + * @returns {Object} Returns `object`. + * @example + * + * var object = { 'a': [{ 'b': { 'c': 3 } }] }; + * + * _.update(object, 'a[0].b.c', function(n) { return n * n; }); + * console.log(object.a[0].b.c); + * // => 9 + * + * _.update(object, 'x[0].y.z', function(n) { return n ? n + 1 : 0; }); + * console.log(object.x[0].y.z); + * // => 0 + */ + function update(object, path, updater) { + return object == null ? object : baseUpdate(object, path, castFunction(updater)); + } + + /** + * This method is like `_.update` except that it accepts `customizer` which is + * invoked to produce the objects of `path`. If `customizer` returns `undefined` + * path creation is handled by the method instead. The `customizer` is invoked + * with three arguments: (nsValue, key, nsObject). + * + * **Note:** This method mutates `object`. + * + * @static + * @memberOf _ + * @since 4.6.0 + * @category Object + * @param {Object} object The object to modify. + * @param {Array|string} path The path of the property to set. + * @param {Function} updater The function to produce the updated value. + * @param {Function} [customizer] The function to customize assigned values. + * @returns {Object} Returns `object`. + * @example + * + * var object = {}; + * + * _.updateWith(object, '[0][1]', _.constant('a'), Object); + * // => { '0': { '1': 'a' } } + */ + function updateWith(object, path, updater, customizer) { + customizer = typeof customizer == 'function' ? customizer : undefined; + return object == null ? object : baseUpdate(object, path, castFunction(updater), customizer); + } + + /** + * Creates an array of the own enumerable string keyed property values of `object`. + * + * **Note:** Non-object values are coerced to objects. + * + * @static + * @since 0.1.0 + * @memberOf _ + * @category Object + * @param {Object} object The object to query. + * @returns {Array} Returns the array of property values. + * @example + * + * function Foo() { + * this.a = 1; + * this.b = 2; + * } + * + * Foo.prototype.c = 3; + * + * _.values(new Foo); + * // => [1, 2] (iteration order is not guaranteed) + * + * _.values('hi'); + * // => ['h', 'i'] + */ + function values(object) { + return object == null ? [] : baseValues(object, keys(object)); + } + + /** + * Creates an array of the own and inherited enumerable string keyed property + * values of `object`. + * + * **Note:** Non-object values are coerced to objects. + * + * @static + * @memberOf _ + * @since 3.0.0 + * @category Object + * @param {Object} object The object to query. + * @returns {Array} Returns the array of property values. + * @example + * + * function Foo() { + * this.a = 1; + * this.b = 2; + * } + * + * Foo.prototype.c = 3; + * + * _.valuesIn(new Foo); + * // => [1, 2, 3] (iteration order is not guaranteed) + */ + function valuesIn(object) { + return object == null ? [] : baseValues(object, keysIn(object)); + } + + /*------------------------------------------------------------------------*/ + + /** + * Clamps `number` within the inclusive `lower` and `upper` bounds. + * + * @static + * @memberOf _ + * @since 4.0.0 + * @category Number + * @param {number} number The number to clamp. + * @param {number} [lower] The lower bound. + * @param {number} upper The upper bound. + * @returns {number} Returns the clamped number. + * @example + * + * _.clamp(-10, -5, 5); + * // => -5 + * + * _.clamp(10, -5, 5); + * // => 5 + */ + function clamp(number, lower, upper) { + if (upper === undefined) { + upper = lower; + lower = undefined; + } + if (upper !== undefined) { + upper = toNumber(upper); + upper = upper === upper ? upper : 0; + } + if (lower !== undefined) { + lower = toNumber(lower); + lower = lower === lower ? lower : 0; + } + return baseClamp(toNumber(number), lower, upper); + } + + /** + * Checks if `n` is between `start` and up to, but not including, `end`. If + * `end` is not specified, it's set to `start` with `start` then set to `0`. + * If `start` is greater than `end` the params are swapped to support + * negative ranges. + * + * @static + * @memberOf _ + * @since 3.3.0 + * @category Number + * @param {number} number The number to check. + * @param {number} [start=0] The start of the range. + * @param {number} end The end of the range. + * @returns {boolean} Returns `true` if `number` is in the range, else `false`. + * @see _.range, _.rangeRight + * @example + * + * _.inRange(3, 2, 4); + * // => true + * + * _.inRange(4, 8); + * // => true + * + * _.inRange(4, 2); + * // => false + * + * _.inRange(2, 2); + * // => false + * + * _.inRange(1.2, 2); + * // => true + * + * _.inRange(5.2, 4); + * // => false + * + * _.inRange(-3, -2, -6); + * // => true + */ + function inRange(number, start, end) { + start = toFinite(start); + if (end === undefined) { + end = start; + start = 0; + } else { + end = toFinite(end); + } + number = toNumber(number); + return baseInRange(number, start, end); + } + + /** + * Produces a random number between the inclusive `lower` and `upper` bounds. + * If only one argument is provided a number between `0` and the given number + * is returned. If `floating` is `true`, or either `lower` or `upper` are + * floats, a floating-point number is returned instead of an integer. + * + * **Note:** JavaScript follows the IEEE-754 standard for resolving + * floating-point values which can produce unexpected results. + * + * @static + * @memberOf _ + * @since 0.7.0 + * @category Number + * @param {number} [lower=0] The lower bound. + * @param {number} [upper=1] The upper bound. + * @param {boolean} [floating] Specify returning a floating-point number. + * @returns {number} Returns the random number. + * @example + * + * _.random(0, 5); + * // => an integer between 0 and 5 + * + * _.random(5); + * // => also an integer between 0 and 5 + * + * _.random(5, true); + * // => a floating-point number between 0 and 5 + * + * _.random(1.2, 5.2); + * // => a floating-point number between 1.2 and 5.2 + */ + function random(lower, upper, floating) { + if (floating && typeof floating != 'boolean' && isIterateeCall(lower, upper, floating)) { + upper = floating = undefined; + } + if (floating === undefined) { + if (typeof upper == 'boolean') { + floating = upper; + upper = undefined; + } + else if (typeof lower == 'boolean') { + floating = lower; + lower = undefined; + } + } + if (lower === undefined && upper === undefined) { + lower = 0; + upper = 1; + } + else { + lower = toFinite(lower); + if (upper === undefined) { + upper = lower; + lower = 0; + } else { + upper = toFinite(upper); + } + } + if (lower > upper) { + var temp = lower; + lower = upper; + upper = temp; + } + if (floating || lower % 1 || upper % 1) { + var rand = nativeRandom(); + return nativeMin(lower + (rand * (upper - lower + freeParseFloat('1e-' + ((rand + '').length - 1)))), upper); + } + return baseRandom(lower, upper); + } + + /*------------------------------------------------------------------------*/ + + /** + * Converts `string` to [camel case](https://en.wikipedia.org/wiki/CamelCase). + * + * @static + * @memberOf _ + * @since 3.0.0 + * @category String + * @param {string} [string=''] The string to convert. + * @returns {string} Returns the camel cased string. + * @example + * + * _.camelCase('Foo Bar'); + * // => 'fooBar' + * + * _.camelCase('--foo-bar--'); + * // => 'fooBar' + * + * _.camelCase('__FOO_BAR__'); + * // => 'fooBar' + */ + var camelCase = createCompounder(function(result, word, index) { + word = word.toLowerCase(); + return result + (index ? capitalize(word) : word); + }); + + /** + * Converts the first character of `string` to upper case and the remaining + * to lower case. + * + * @static + * @memberOf _ + * @since 3.0.0 + * @category String + * @param {string} [string=''] The string to capitalize. + * @returns {string} Returns the capitalized string. + * @example + * + * _.capitalize('FRED'); + * // => 'Fred' + */ + function capitalize(string) { + return upperFirst(toString(string).toLowerCase()); + } + + /** + * Deburrs `string` by converting + * [Latin-1 Supplement](https://en.wikipedia.org/wiki/Latin-1_Supplement_(Unicode_block)#Character_table) + * and [Latin Extended-A](https://en.wikipedia.org/wiki/Latin_Extended-A) + * letters to basic Latin letters and removing + * [combining diacritical marks](https://en.wikipedia.org/wiki/Combining_Diacritical_Marks). + * + * @static + * @memberOf _ + * @since 3.0.0 + * @category String + * @param {string} [string=''] The string to deburr. + * @returns {string} Returns the deburred string. + * @example + * + * _.deburr('déjà vu'); + * // => 'deja vu' + */ + function deburr(string) { + string = toString(string); + return string && string.replace(reLatin, deburrLetter).replace(reComboMark, ''); + } + + /** + * Checks if `string` ends with the given target string. + * + * @static + * @memberOf _ + * @since 3.0.0 + * @category String + * @param {string} [string=''] The string to inspect. + * @param {string} [target] The string to search for. + * @param {number} [position=string.length] The position to search up to. + * @returns {boolean} Returns `true` if `string` ends with `target`, + * else `false`. + * @example + * + * _.endsWith('abc', 'c'); + * // => true + * + * _.endsWith('abc', 'b'); + * // => false + * + * _.endsWith('abc', 'b', 2); + * // => true + */ + function endsWith(string, target, position) { + string = toString(string); + target = baseToString(target); + + var length = string.length; + position = position === undefined + ? length + : baseClamp(toInteger(position), 0, length); + + var end = position; + position -= target.length; + return position >= 0 && string.slice(position, end) == target; + } + + /** + * Converts the characters "&", "<", ">", '"', and "'" in `string` to their + * corresponding HTML entities. + * + * **Note:** No other characters are escaped. To escape additional + * characters use a third-party library like [_he_](https://mths.be/he). + * + * Though the ">" character is escaped for symmetry, characters like + * ">" and "/" don't need escaping in HTML and have no special meaning + * unless they're part of a tag or unquoted attribute value. See + * [Mathias Bynens's article](https://mathiasbynens.be/notes/ambiguous-ampersands) + * (under "semi-related fun fact") for more details. + * + * When working with HTML you should always + * [quote attribute values](http://wonko.com/post/html-escaping) to reduce + * XSS vectors. + * + * @static + * @since 0.1.0 + * @memberOf _ + * @category String + * @param {string} [string=''] The string to escape. + * @returns {string} Returns the escaped string. + * @example + * + * _.escape('fred, barney, & pebbles'); + * // => 'fred, barney, & pebbles' + */ + function escape(string) { + string = toString(string); + return (string && reHasUnescapedHtml.test(string)) + ? string.replace(reUnescapedHtml, escapeHtmlChar) + : string; + } + + /** + * Escapes the `RegExp` special characters "^", "$", "\", ".", "*", "+", + * "?", "(", ")", "[", "]", "{", "}", and "|" in `string`. + * + * @static + * @memberOf _ + * @since 3.0.0 + * @category String + * @param {string} [string=''] The string to escape. + * @returns {string} Returns the escaped string. + * @example + * + * _.escapeRegExp('[lodash](https://lodash.com/)'); + * // => '\[lodash\]\(https://lodash\.com/\)' + */ + function escapeRegExp(string) { + string = toString(string); + return (string && reHasRegExpChar.test(string)) + ? string.replace(reRegExpChar, '\\$&') + : string; + } + + /** + * Converts `string` to + * [kebab case](https://en.wikipedia.org/wiki/Letter_case#Special_case_styles). + * + * @static + * @memberOf _ + * @since 3.0.0 + * @category String + * @param {string} [string=''] The string to convert. + * @returns {string} Returns the kebab cased string. + * @example + * + * _.kebabCase('Foo Bar'); + * // => 'foo-bar' + * + * _.kebabCase('fooBar'); + * // => 'foo-bar' + * + * _.kebabCase('__FOO_BAR__'); + * // => 'foo-bar' + */ + var kebabCase = createCompounder(function(result, word, index) { + return result + (index ? '-' : '') + word.toLowerCase(); + }); + + /** + * Converts `string`, as space separated words, to lower case. + * + * @static + * @memberOf _ + * @since 4.0.0 + * @category String + * @param {string} [string=''] The string to convert. + * @returns {string} Returns the lower cased string. + * @example + * + * _.lowerCase('--Foo-Bar--'); + * // => 'foo bar' + * + * _.lowerCase('fooBar'); + * // => 'foo bar' + * + * _.lowerCase('__FOO_BAR__'); + * // => 'foo bar' + */ + var lowerCase = createCompounder(function(result, word, index) { + return result + (index ? ' ' : '') + word.toLowerCase(); + }); + + /** + * Converts the first character of `string` to lower case. + * + * @static + * @memberOf _ + * @since 4.0.0 + * @category String + * @param {string} [string=''] The string to convert. + * @returns {string} Returns the converted string. + * @example + * + * _.lowerFirst('Fred'); + * // => 'fred' + * + * _.lowerFirst('FRED'); + * // => 'fRED' + */ + var lowerFirst = createCaseFirst('toLowerCase'); + + /** + * Pads `string` on the left and right sides if it's shorter than `length`. + * Padding characters are truncated if they can't be evenly divided by `length`. + * + * @static + * @memberOf _ + * @since 3.0.0 + * @category String + * @param {string} [string=''] The string to pad. + * @param {number} [length=0] The padding length. + * @param {string} [chars=' '] The string used as padding. + * @returns {string} Returns the padded string. + * @example + * + * _.pad('abc', 8); + * // => ' abc ' + * + * _.pad('abc', 8, '_-'); + * // => '_-abc_-_' + * + * _.pad('abc', 3); + * // => 'abc' + */ + function pad(string, length, chars) { + string = toString(string); + length = toInteger(length); + + var strLength = length ? stringSize(string) : 0; + if (!length || strLength >= length) { + return string; + } + var mid = (length - strLength) / 2; + return ( + createPadding(nativeFloor(mid), chars) + + string + + createPadding(nativeCeil(mid), chars) + ); + } + + /** + * Pads `string` on the right side if it's shorter than `length`. Padding + * characters are truncated if they exceed `length`. + * + * @static + * @memberOf _ + * @since 4.0.0 + * @category String + * @param {string} [string=''] The string to pad. + * @param {number} [length=0] The padding length. + * @param {string} [chars=' '] The string used as padding. + * @returns {string} Returns the padded string. + * @example + * + * _.padEnd('abc', 6); + * // => 'abc ' + * + * _.padEnd('abc', 6, '_-'); + * // => 'abc_-_' + * + * _.padEnd('abc', 3); + * // => 'abc' + */ + function padEnd(string, length, chars) { + string = toString(string); + length = toInteger(length); + + var strLength = length ? stringSize(string) : 0; + return (length && strLength < length) + ? (string + createPadding(length - strLength, chars)) + : string; + } + + /** + * Pads `string` on the left side if it's shorter than `length`. Padding + * characters are truncated if they exceed `length`. + * + * @static + * @memberOf _ + * @since 4.0.0 + * @category String + * @param {string} [string=''] The string to pad. + * @param {number} [length=0] The padding length. + * @param {string} [chars=' '] The string used as padding. + * @returns {string} Returns the padded string. + * @example + * + * _.padStart('abc', 6); + * // => ' abc' + * + * _.padStart('abc', 6, '_-'); + * // => '_-_abc' + * + * _.padStart('abc', 3); + * // => 'abc' + */ + function padStart(string, length, chars) { + string = toString(string); + length = toInteger(length); + + var strLength = length ? stringSize(string) : 0; + return (length && strLength < length) + ? (createPadding(length - strLength, chars) + string) + : string; + } + + /** + * Converts `string` to an integer of the specified radix. If `radix` is + * `undefined` or `0`, a `radix` of `10` is used unless `value` is a + * hexadecimal, in which case a `radix` of `16` is used. + * + * **Note:** This method aligns with the + * [ES5 implementation](https://es5.github.io/#x15.1.2.2) of `parseInt`. + * + * @static + * @memberOf _ + * @since 1.1.0 + * @category String + * @param {string} string The string to convert. + * @param {number} [radix=10] The radix to interpret `value` by. + * @param- {Object} [guard] Enables use as an iteratee for methods like `_.map`. + * @returns {number} Returns the converted integer. + * @example + * + * _.parseInt('08'); + * // => 8 + * + * _.map(['6', '08', '10'], _.parseInt); + * // => [6, 8, 10] + */ + function parseInt(string, radix, guard) { + if (guard || radix == null) { + radix = 0; + } else if (radix) { + radix = +radix; + } + return nativeParseInt(toString(string).replace(reTrimStart, ''), radix || 0); + } + + /** + * Repeats the given string `n` times. + * + * @static + * @memberOf _ + * @since 3.0.0 + * @category String + * @param {string} [string=''] The string to repeat. + * @param {number} [n=1] The number of times to repeat the string. + * @param- {Object} [guard] Enables use as an iteratee for methods like `_.map`. + * @returns {string} Returns the repeated string. + * @example + * + * _.repeat('*', 3); + * // => '***' + * + * _.repeat('abc', 2); + * // => 'abcabc' + * + * _.repeat('abc', 0); + * // => '' + */ + function repeat(string, n, guard) { + if ((guard ? isIterateeCall(string, n, guard) : n === undefined)) { + n = 1; + } else { + n = toInteger(n); + } + return baseRepeat(toString(string), n); + } + + /** + * Replaces matches for `pattern` in `string` with `replacement`. + * + * **Note:** This method is based on + * [`String#replace`](https://mdn.io/String/replace). + * + * @static + * @memberOf _ + * @since 4.0.0 + * @category String + * @param {string} [string=''] The string to modify. + * @param {RegExp|string} pattern The pattern to replace. + * @param {Function|string} replacement The match replacement. + * @returns {string} Returns the modified string. + * @example + * + * _.replace('Hi Fred', 'Fred', 'Barney'); + * // => 'Hi Barney' + */ + function replace() { + var args = arguments, + string = toString(args[0]); + + return args.length < 3 ? string : string.replace(args[1], args[2]); + } + + /** + * Converts `string` to + * [snake case](https://en.wikipedia.org/wiki/Snake_case). + * + * @static + * @memberOf _ + * @since 3.0.0 + * @category String + * @param {string} [string=''] The string to convert. + * @returns {string} Returns the snake cased string. + * @example + * + * _.snakeCase('Foo Bar'); + * // => 'foo_bar' + * + * _.snakeCase('fooBar'); + * // => 'foo_bar' + * + * _.snakeCase('--FOO-BAR--'); + * // => 'foo_bar' + */ + var snakeCase = createCompounder(function(result, word, index) { + return result + (index ? '_' : '') + word.toLowerCase(); + }); + + /** + * Splits `string` by `separator`. + * + * **Note:** This method is based on + * [`String#split`](https://mdn.io/String/split). + * + * @static + * @memberOf _ + * @since 4.0.0 + * @category String + * @param {string} [string=''] The string to split. + * @param {RegExp|string} separator The separator pattern to split by. + * @param {number} [limit] The length to truncate results to. + * @returns {Array} Returns the string segments. + * @example + * + * _.split('a-b-c', '-', 2); + * // => ['a', 'b'] + */ + function split(string, separator, limit) { + if (limit && typeof limit != 'number' && isIterateeCall(string, separator, limit)) { + separator = limit = undefined; + } + limit = limit === undefined ? MAX_ARRAY_LENGTH : limit >>> 0; + if (!limit) { + return []; + } + string = toString(string); + if (string && ( + typeof separator == 'string' || + (separator != null && !isRegExp(separator)) + )) { + separator = baseToString(separator); + if (!separator && hasUnicode(string)) { + return castSlice(stringToArray(string), 0, limit); + } + } + return string.split(separator, limit); + } + + /** + * Converts `string` to + * [start case](https://en.wikipedia.org/wiki/Letter_case#Stylistic_or_specialised_usage). + * + * @static + * @memberOf _ + * @since 3.1.0 + * @category String + * @param {string} [string=''] The string to convert. + * @returns {string} Returns the start cased string. + * @example + * + * _.startCase('--foo-bar--'); + * // => 'Foo Bar' + * + * _.startCase('fooBar'); + * // => 'Foo Bar' + * + * _.startCase('__FOO_BAR__'); + * // => 'FOO BAR' + */ + var startCase = createCompounder(function(result, word, index) { + return result + (index ? ' ' : '') + upperFirst(word); + }); + + /** + * Checks if `string` starts with the given target string. + * + * @static + * @memberOf _ + * @since 3.0.0 + * @category String + * @param {string} [string=''] The string to inspect. + * @param {string} [target] The string to search for. + * @param {number} [position=0] The position to search from. + * @returns {boolean} Returns `true` if `string` starts with `target`, + * else `false`. + * @example + * + * _.startsWith('abc', 'a'); + * // => true + * + * _.startsWith('abc', 'b'); + * // => false + * + * _.startsWith('abc', 'b', 1); + * // => true + */ + function startsWith(string, target, position) { + string = toString(string); + position = position == null + ? 0 + : baseClamp(toInteger(position), 0, string.length); + + target = baseToString(target); + return string.slice(position, position + target.length) == target; + } + + /** + * Creates a compiled template function that can interpolate data properties + * in "interpolate" delimiters, HTML-escape interpolated data properties in + * "escape" delimiters, and execute JavaScript in "evaluate" delimiters. Data + * properties may be accessed as free variables in the template. If a setting + * object is given, it takes precedence over `_.templateSettings` values. + * + * **Note:** In the development build `_.template` utilizes + * [sourceURLs](http://www.html5rocks.com/en/tutorials/developertools/sourcemaps/#toc-sourceurl) + * for easier debugging. + * + * For more information on precompiling templates see + * [lodash's custom builds documentation](https://lodash.com/custom-builds). + * + * For more information on Chrome extension sandboxes see + * [Chrome's extensions documentation](https://developer.chrome.com/extensions/sandboxingEval). + * + * @static + * @since 0.1.0 + * @memberOf _ + * @category String + * @param {string} [string=''] The template string. + * @param {Object} [options={}] The options object. + * @param {RegExp} [options.escape=_.templateSettings.escape] + * The HTML "escape" delimiter. + * @param {RegExp} [options.evaluate=_.templateSettings.evaluate] + * The "evaluate" delimiter. + * @param {Object} [options.imports=_.templateSettings.imports] + * An object to import into the template as free variables. + * @param {RegExp} [options.interpolate=_.templateSettings.interpolate] + * The "interpolate" delimiter. + * @param {string} [options.sourceURL='lodash.templateSources[n]'] + * The sourceURL of the compiled template. + * @param {string} [options.variable='obj'] + * The data object variable name. + * @param- {Object} [guard] Enables use as an iteratee for methods like `_.map`. + * @returns {Function} Returns the compiled template function. + * @example + * + * // Use the "interpolate" delimiter to create a compiled template. + * var compiled = _.template('hello <%= user %>!'); + * compiled({ 'user': 'fred' }); + * // => 'hello fred!' + * + * // Use the HTML "escape" delimiter to escape data property values. + * var compiled = _.template('<%- value %>'); + * compiled({ 'value': '
+

Gene Signatures

@@ -145,27 +151,30 @@

1. Creating a Signature object in R

Once a set of genes that are up or down regulated in the process or cell type of interest are selected, creating a Signature object from them is relatively straightforward:

-
sigData <- c(
-    Gene.A = 1, Gene.B = 1, Gene.C = 1,
-    Gene.D = -1, Gene.B = -1, Gene.C = -1
-)
+
+sigData <- c(
+    Gene.A = 1, Gene.B = 1, Gene.C = 1,
+    Gene.D = -1, Gene.B = -1, Gene.C = -1
+)
 
-sig <- createGeneSignature(name = "Interesting Process", sigData = sigData)

+sig <- createGeneSignature(name = "Interesting Process", sigData = sigData)

For the sigData vector, the names represent gene names and the values (1 or -1) represent the ‘sign’ of the gene. For an unsigned signature, just use 1 for the value of every gene.

A list of these sig objects can then be passed into the VISION object constructor instead of paths to .gmt files.

-
sig1 <- createGeneSignature(name = "Interesting Process", ... )
-sig2 <- createGeneSignature(name = "Another Interesting Process", ... )
+
+sig1 <- createGeneSignature(name = "Interesting Process", ... )
+sig2 <- createGeneSignature(name = "Another Interesting Process", ... )
 
-mySignatures <- c(sig1, sig2)
+mySignatures <- c(sig1, sig2)
 
-vis <- Vision(data = expressionMat, signatures = mySignatures)

+vis <- Vision(data = expressionMat, signatures = mySignatures)

Additionally, you can mix and match user-created signatures and paths to signature files in the signatures argument. When doing this, signatures in each library file are read and combined with the user-created signatures.

-
sig1 <- createGeneSignature(name = "Interesting Process", ... )
-sig2 <- createGeneSignature(name = "Another Interesting Process", ... )
+
+sig1 <- createGeneSignature(name = "Interesting Process", ... )
+sig2 <- createGeneSignature(name = "Another Interesting Process", ... )
 
-mySignatures <- c(sig1, sig2, 'path/to/some/library.gmt')
+mySignatures <- c(sig1, sig2, 'path/to/some/library.gmt')
 
-vis <- Vision(data = expressionMat, signatures = mySignatures)

+vis <- Vision(data = expressionMat, signatures = mySignatures)

@@ -218,11 +227,11 @@

-

Developed by Matt Jones, David Detomaso, Tal Ashuach.

+

Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

-

Site built with pkgdown 1.5.1.

+

Site built with pkgdown 1.6.1.

diff --git a/docs/articles/VISION-vignette.html b/docs/articles/VISION-vignette.html index 804a440a..05701333 100644 --- a/docs/articles/VISION-vignette.html +++ b/docs/articles/VISION-vignette.html @@ -47,7 +47,7 @@
  • - +
    • @@ -73,6 +73,12 @@
  • Incorporating a Trajectory Model
    • +
  • + PhyloVision and Hotspot +
    • +
  • + Spatial Data and Hotspot +
  • How To: Working with Seurat
    • @@ -91,7 +97,7 @@
    • - +
      • @@ -105,7 +111,7 @@ -
      +

      Introduction to VISION

      @@ -122,9 +128,10 @@

      Introduction to VISION

      Preliminaries

      If you have yet to install VISION, we recommend installing the package from Github to install this package. Full source code can be found at the VISION Github repository, available here.

      -
      require(devtools)
-install_github("YosefLab/VISION")
      -

      Once VISION and R are installed, you may load in VISION using library(VISION).

      +
      +require(devtools)
+install_github("YosefLab/VISION")
      +

      Once VISION and R are installed, you may load in VISION using library(VISION).

      @@ -140,26 +147,27 @@

      Creating the VISION object

      Creating the VISION object requires a gene expression matrix and either a list of Gene Signatures or a data.frame of meta-data.

      In this example - both are provided.

      -
      # Load VISION
-library(VISION)
+
      +# Load VISION
+library(VISION)
 
 # Read in expression counts (Genes X Cells)
-counts <- read.table("data/expression_counts.txt.gz",
-                     header = TRUE,
-                     sep = '\t',
-                     row.names = 1)
+counts <- read.table("data/expression_counts.txt.gz",
+                     header = TRUE,
+                     sep = '\t',
+                     row.names = 1)
 
 # Scale counts within a sample
-n.umi <- colSums(counts)
+n.umi <- colSums(counts)
 
-scaled_counts <- t(t(counts) / n.umi) * median(n.umi)
+scaled_counts <- t(t(counts) / n.umi) * median(n.umi)
 
 # Read in meta data (Cells x Vars)
-meta = read.table("data/glio_meta.txt.gz", sep='\t', header=T, row.names=1)
+meta = read.table("data/glio_meta.txt.gz", sep='\t', header=T, row.names=1)
 
-vis <- Vision(scaled_counts,
-              signatures = c("data/h.all.v5.2.symbols.gmt"),
-              meta = meta)
      
+vis <- Vision(scaled_counts,
+              signatures = c("data/h.all.v5.2.symbols.gmt"),
+              meta = meta)

      Expression Data

      The provided expression data should be scaled and normalized. The example above shows just a simple UMI-scaling, but it is recommended to apply more advanced normalization procedures such as batch correction or removal of technical confounders.

      The expression data should not be log-transformed prior to loading into VISION.

      @@ -176,31 +184,34 @@

      Running an Analysis

      To run an analysis, simply call the analyze function:

      -
      # Set the number of threads when running parallel computations
-options(mc.cores = 2)
+
      +# Set the number of threads when running parallel computations
+options(mc.cores = 2)
 
-vis <- analyze(vis)
      
+vis <- analyze(vis)

      Viewing Results

      -

      With the processed Vision object, a dynamic web report can be generated with the viewResults() function.

      - +

      With the processed Vision object, a dynamic web report can be generated with the viewResults() function.

      +

      This will launch a browser running the interactive report.

      Other options (port, host, browser) can be provided to control how this occurs. For example, if you are launching a report on a remote server (such as an AWS instance) and want to make it accessible to others, run this with host="0.0.0.0", some selected port number (e.g. port=8888), and browser=FALSE (so a browser isn’t auto-opened). Then the report should be available at “<your instance IP address>:8888”. (Note: You will also likely need to enable inbound traffic on your selected port for this to work correctly).

      Alternately, you can work with the VISION object directly in R. For example:

      -
      # Display autocorrelation coefficients for signatures
-head(vis@SigConsistencyScores@sigProjMatrix)
+
      +# Display autocorrelation coefficients for signatures
+head(vis@SigConsistencyScores@sigProjMatrix)
 
 # View autocorrelation empirical p-values
-head(vis@SigConsistencyScores@emp_pMatrix)
+head(vis@SigConsistencyScores@emp_pMatrix)
 
 # Plot signature scores for a signature of interest
-tsne <- vis@Projections$tSNE30
-sigScores <- vis@sigScores[, "HALLMARK_INTERFERON_GAMMA_RESPONSE"]
+tsne <- vis@Projections$tSNE30
+sigScores <- vis@sigScores[, "HALLMARK_INTERFERON_GAMMA_RESPONSE"]
 
-library(ggplot2)
-ggplot() + aes(x=tsne[, 1], y=tsne[, 2], color=sigScores) + geom_point()
      
+library(ggplot2)
+ggplot() + aes(x=tsne[, 1], y=tsne[, 2], color=sigScores) + geom_point()

      For more details on the structure of the VISION object see XXX.

      @@ -243,12 +254,13 @@

      Adding 2d Projections

      Two-dimensional projections are used to visualize the data in the output report.

      By default, VISION computes tSNE on the latent space for visualization. However, other options are availabled via the projection_methods argument.

      -

      Often times, users will have pre-computed projections that they would like to use for visualizing their data (e.g. a pre-computed tSNE, or UMAP projection). In this case, the addProjection() method can be used to add this view of the data to the output report.

      -
      projection <- read.csv("umap_results.csv")
+
      Often times, users will have pre-computed projections that they would like to use for visualizing their data (e.g. a pre-computed tSNE, or UMAP projection). In this case, the addProjection() method can be used to add this view of the data to the output report.
      
+
      +projection <- read.csv("umap_results.csv")
 
 # projection is a matirx or data.frame of dimension (Cells x 2)
 
-vis <- addProjection(vis, "UMAP", projection)
      
+vis <- addProjection(vis, "UMAP", projection)
      @@ -264,11 +276,11 @@

      -

      Developed by Matt Jones, David Detomaso, Tal Ashuach.

      +

      Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

      -

      Site built with pkgdown 1.5.1.

      +

      Site built with pkgdown 1.6.1.

      diff --git a/docs/articles/index.html b/docs/articles/index.html index b371a436..ac358c20 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -89,7 +89,7 @@
      • - +
        • @@ -115,6 +115,12 @@
      • Incorporating a Trajectory Model
        • +
      • + PhyloVision and Hotspot +
        • +
      • + Spatial Data and Hotspot +
      • How To: Working with Seurat
        • @@ -133,7 +139,7 @@
        • - +
          • @@ -164,6 +170,10 @@

          All vignettes

          Micropooling
          +
          VisCas Vignette
          +
          +
          Vision Hotspot Vignette
          +
          Incorporating a Trajectory Model
          How To: Loading 10x CellRanger Outputs
          @@ -180,11 +190,11 @@

          All vignettes

          -

          Developed by Matt Jones, David Detomaso, Tal Ashuach.

          +

          Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

          -

          Site built with pkgdown 1.5.1.

          +

          Site built with pkgdown 1.6.1.

          diff --git a/docs/articles/micropooling.html b/docs/articles/micropooling.html index e8921fe6..de283f9c 100644 --- a/docs/articles/micropooling.html +++ b/docs/articles/micropooling.html @@ -47,7 +47,7 @@
          • - +
            • @@ -73,6 +73,12 @@
          • Incorporating a Trajectory Model
            • +
          • + PhyloVision and Hotspot +
            • +
          • + Spatial Data and Hotspot +
          • How To: Working with Seurat
            • @@ -91,7 +97,7 @@
            • - +
              • @@ -105,7 +111,7 @@ -
              +

              Micropooling

              @@ -152,58 +158,58 @@

              Workflow

              Here, we’ll demonstrate a common use case of micropooling on the data:

              -
              library(VISION)
-
-counts = as.matrix(read.table("data/hemato_counts.csv.gz", sep=',', header=T, row.names=1))
-
-# compute scaled counts
-scale.factor = median(colSums(counts))
-scaled.counts = t(t(counts) / colSums(counts)) * scale.factor
-
-# read in meta data
-meta = read.table("data/hemato_covariates.txt.gz", sep='\t', header=T, row.names=1)
-meta = meta[colnames(scaled.counts), -1]
-
-vis <- Vision(scaled.counts, meta = meta
-              signatures = c("data/h.all.v5.2.symbols.gmt"),
-              pool = T, cellsPerPartition = 5)
-
-vis <- analyze(vis)
-
-viewResults(vis)
              +
              library(VISION)
+
+counts = as.matrix(read.table("data/hemato_counts.csv.gz", sep=',', header=T, row.names=1))
+
+# compute scaled counts
+scale.factor = median(colSums(counts))
+scaled.counts = t(t(counts) / colSums(counts)) * scale.factor
+
+# read in meta data
+meta = read.table("data/hemato_covariates.txt.gz", sep='\t', header=T, row.names=1)
+meta = meta[colnames(scaled.counts), -1]
+
+vis <- Vision(scaled.counts, meta = meta
+              signatures = c("data/h.all.v5.2.symbols.gmt"),
+              pool = T, cellsPerPartition = 5)
+
+vis <- analyze(vis)
+
+viewResults(vis)

              Micropooling independently of the main VISION analysis

              -

              There may be reasons it is desired micropool outside of the main VISION analyze() function. For example, there may be discrete classes that users may not wish to pool across (e.g. not wanting to merge disease and control cells). Or, you may want to only use the micropooling function independently of the rest of the pipeline. This can be accomplished using the applyMicroClustering() utility function as demonstrated here.

              -
              ## Create scaled.counts and meta as shown above
-
-pools <- applyMicroClustering(scaled.counts, cellsPerPartition = 5)
-
-# Create pooled versions of expression matrix and meta-data
-pooledExpression <- poolMatrixCols(scaled.counts, pools)
-pooledMeta <- poolMetaData(meta, pools)
-
-# These could then be fed into the VISION constructor
-vis <- Vision(pooledExpression, meta = pooledMeta
-              signatures = c("data/h.all.v5.2.symbols.gmt"))
              +

              There may be reasons it is desired micropool outside of the main VISION analyze() function. For example, there may be discrete classes that users may not wish to pool across (e.g. not wanting to merge disease and control cells). Or, you may want to only use the micropooling function independently of the rest of the pipeline. This can be accomplished using the applyMicroClustering() utility function as demonstrated here.

              +
              ## Create scaled.counts and meta as shown above
+
+pools <- applyMicroClustering(scaled.counts, cellsPerPartition = 5)
+
+# Create pooled versions of expression matrix and meta-data
+pooledExpression <- poolMatrixCols(scaled.counts, pools)
+pooledMeta <- poolMetaData(meta, pools)
+
+# These could then be fed into the VISION constructor
+vis <- Vision(pooledExpression, meta = pooledMeta
+              signatures = c("data/h.all.v5.2.symbols.gmt"))

              Alternately, if you already have a latent space computed and wish to use this (instead of PCA) when pooling outside of the normal Vision pipeline, you can provide it when calling applyMicroClustering() and later pool the latent space.

              This is demonstrated below:

              -
              ## Create scaled.counts and meta as shown above
-
-pools <- applyMicroClustering(scaled.counts,
-    cellsPerPartition = 5, latentSpace = latentPpace)
-
-# Create pooled versions of expression matrix and meta-data
-pooledExpression <- poolMatrixCols(scaled.counts, pools)
-pooledMeta <- poolMetaData(meta, pools)
-pooledLatentSpace <- poolMatrixRows(latentSpace, pools)
-
-# These could then be fed into the VISION constructor
-vis <- Vision(pooledExpression, meta = pooledMeta
-              signatures = c("data/h.all.v5.2.symbols.gmt"),
-              latentSpace = pooledLatentSpace)
              +
              ## Create scaled.counts and meta as shown above
+
+pools <- applyMicroClustering(scaled.counts,
+    cellsPerPartition = 5, latentSpace = latentPpace)
+
+# Create pooled versions of expression matrix and meta-data
+pooledExpression <- poolMatrixCols(scaled.counts, pools)
+pooledMeta <- poolMetaData(meta, pools)
+pooledLatentSpace <- poolMatrixRows(latentSpace, pools)
+
+# These could then be fed into the VISION constructor
+vis <- Vision(pooledExpression, meta = pooledMeta
+              signatures = c("data/h.all.v5.2.symbols.gmt"),
+              latentSpace = pooledLatentSpace)
              @@ -218,11 +224,11 @@

              -

              Developed by Matt Jones, David Detomaso, Tal Ashuach.

              +

              Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

              -

              Site built with pkgdown 1.5.1.

              +

              Site built with pkgdown 1.6.1.

              diff --git a/docs/articles/trajectories.html b/docs/articles/trajectories.html index 330e7f36..875204a5 100644 --- a/docs/articles/trajectories.html +++ b/docs/articles/trajectories.html @@ -47,7 +47,7 @@
              • - +
                • @@ -73,6 +73,12 @@
              • Incorporating a Trajectory Model
                • +
              • + PhyloVision and Hotspot +
                • +
              • + Spatial Data and Hotspot +
              • How To: Working with Seurat
                • @@ -91,7 +97,7 @@
                • - +
                  • @@ -105,7 +111,7 @@ -
                  +

                  Incorporating a Trajectory Model

                  @@ -132,9 +138,10 @@

                  Installation

                  You should have a working installation of VISION, dyno, and tidyverse.

                  -
                  devtools::install_github("YosefLab/VISION")
-devtools::install_github("dynverse/dyno")
-install.packages('tidyverse')
                  +
                  +devtools::install_github("YosefLab/VISION")
+devtools::install_github("dynverse/dyno")
+install.packages('tidyverse')

                  @@ -146,57 +153,64 @@

                  Workflow

                  We begin by loading in the data and requisite libraries:

                  -
                  library(VISION)
-library(dyno)
-library(tidyverse)
                  -
                  counts = as.matrix(read.table("data/hemato_counts.csv.gz", sep=',', header=T, row.names=1))
                  +
                  +library(VISION)
+library(dyno)
+library(tidyverse)
                  +
                  +counts = as.matrix(read.table("data/hemato_counts.csv.gz", sep=',', header=T, row.names=1))

                  We’ll now follow the dyno vignette in the github README. You’ll need to make sure you have Docker installed. Although we use Slingshot here, there is a wide variety of methods that can be used, as listed on the Dynmethods page.

                  Before running the model, we’ll need to perform some gene filtering. We first only select the genes used in the original Tusi et al study, then for further efficiency, we further filter using VISION’s Fano filtering.

                  -
                  k.genes = read.table("data/bBM.filtered_gene_list.paper.txt.gz", sep=',')[,1]
-filt.counts = counts[k.genes, ]
+
                  +k.genes = read.table("data/bBM.filtered_gene_list.paper.txt.gz", sep=',')[,1]
+filt.counts = counts[k.genes, ]
 
-f.genes = VISION:::filterGenesFano(filt.counts)
-filt.counts = filt.counts[f.genes, ]
                  
+f.genes = VISION:::filterGenesFano(filt.counts)
+filt.counts = filt.counts[f.genes, ]

                  Now, resuming the workflow recommended on the dyno vignette,

                  -
                  umis <- colSums(counts)
-scale.factor <- median(umis)
-expr <- t(t(counts) / umis) * scale.factor
-filt.expr <-  log(1 + expr[f.genes,])
+
                  +umis <- colSums(counts)
+scale.factor <- median(umis)
+expr <- t(t(counts) / umis) * scale.factor
+filt.expr <-  log(1 + expr[f.genes,])
 
-dataset <- wrap_expression(
-  counts = t(filt.counts),
-  expression = t(filt.expr)
-)
+dataset <- wrap_expression(
+  counts = t(filt.counts),
+  expression = t(filt.expr)
+)
 
-model <- infer_trajectory(dataset, "projected_slingshot", verbose=T)
+model <- infer_trajectory(dataset, "projected_slingshot", verbose=T)
 
-model <- model %>% add_dimred(dyndimred::dimred_mds, expression_source = dataset$expression)
+model <- model %>% add_dimred(dyndimred::dimred_mds, expression_source = dataset$expression)
 
-plot_dimred(
-  model,
-  expression_source = dataset$expression
-)
                  
+plot_dimred(
+  model,
+  expression_source = dataset$expression
+)

                  Now, with this model saved we can pass it to VISION via the latentTrajectory parameter. The model will automatically be analyzed with the same signatures passed to the VISION object, and with this model, the Trajectory tab will be activated in the VISION output report.

                  -
                  meta <- read.table("data/hemato_covariates.txt.gz", sep='\t', header=T, row.names=1)
-meta <- meta[colnames(expr), -1]
+
                  +meta <- read.table("data/hemato_covariates.txt.gz", sep='\t', header=T, row.names=1)
+meta <- meta[colnames(expr), -1]
 
-vis <- Vision(expr, signatures = c("data/h.all.v5.2.symbols.gmt"),
-            meta = meta, latentTrajectory = model)
+vis <- Vision(expr, signatures = c("data/h.all.v5.2.symbols.gmt"),
+            meta = meta, latentTrajectory = model)
 
-vis <- addProjection(vis, "MDS", model$dimred[,c(1,2)])
+vis <- addProjection(vis, "MDS", model$dimred[,c(1,2)])
 
-vis <- analyze(vis)
                  
+vis <- analyze(vis)

                  Session Info

                  - -
                  ## R version 4.0.2 (2020-06-22)
-## Platform: x86_64-apple-darwin19.5.0 (64-bit)
-## Running under: macOS Catalina 10.15.5
+
+
                  ## R version 4.0.4 (2021-02-15)
+## Platform: x86_64-apple-darwin19.6.0 (64-bit)
+## Running under: macOS Catalina 10.15.7
 ## 
 ## Matrix products: default
-## BLAS/LAPACK: /usr/local/Cellar/openblas/0.3.10/lib/libopenblasp-r0.3.10.dylib
+## BLAS:   /usr/local/Cellar/openblas/0.3.13/lib/libopenblasp-r0.3.13.dylib
+## LAPACK: /usr/local/Cellar/r/4.0.4_2/lib/R/lib/libRlapack.dylib
 ## 
 ## locale:
 ## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
@@ -205,18 +219,20 @@ 
                  
 ## [1] stats     graphics  grDevices utils     datasets  methods   base     
 ## 
 ## other attached packages:
-## [1] BiocStyle_2.16.0
+## [1] BiocStyle_2.18.1
 ## 
 ## loaded via a namespace (and not attached):
-##  [1] bookdown_0.19       rprojroot_1.3-2     digest_0.6.25      
-##  [4] crayon_1.3.4        assertthat_0.2.1    MASS_7.3-51.6      
-##  [7] R6_2.4.1            backports_1.1.8     magrittr_1.5       
-## [10] evaluate_0.14       stringi_1.4.6       rlang_0.4.6        
-## [13] rstudioapi_0.11     fs_1.4.1            rmarkdown_2.3      
-## [16] pkgdown_1.5.1       desc_1.2.0          tools_4.0.2        
-## [19] stringr_1.4.0       yaml_2.2.1          xfun_0.15          
-## [22] compiler_4.0.2      BiocManager_1.30.10 memoise_1.1.0      
-## [25] htmltools_0.5.0     knitr_1.29
                  
+##  [1] knitr_1.33          magrittr_2.0.1      R6_2.5.0           
+##  [4] ragg_1.1.2          rlang_0.4.11        fastmap_1.1.0      
+##  [7] stringr_1.4.0       tools_4.0.4         xfun_0.23          
+## [10] jquerylib_0.1.4     htmltools_0.5.1.1   systemfonts_1.0.2  
+## [13] yaml_2.2.1          digest_0.6.27       rprojroot_2.0.2    
+## [16] pkgdown_1.6.1       crayon_1.4.1        bookdown_0.22      
+## [19] textshaping_0.3.4   BiocManager_1.30.15 sass_0.4.0         
+## [22] fs_1.5.0            memoise_2.0.0       cachem_1.0.5       
+## [25] evaluate_0.14       rmarkdown_2.8       stringi_1.6.2      
+## [28] compiler_4.0.4      bslib_0.2.5.1       desc_1.3.0         
+## [31] jsonlite_1.7.2
                  @@ -231,11 +247,11 @@

                  -

                  Developed by Matt Jones, David Detomaso, Tal Ashuach.

                  +

                  Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

                  -

                  Site built with pkgdown 1.5.1.

                  +

                  Site built with pkgdown 1.6.1.

                  diff --git a/docs/articles/web_only/10xData.html b/docs/articles/web_only/10xData.html index 7aed9547..22525be5 100644 --- a/docs/articles/web_only/10xData.html +++ b/docs/articles/web_only/10xData.html @@ -47,7 +47,7 @@
                  • - +
                    • @@ -73,6 +73,12 @@
                  • Incorporating a Trajectory Model
                    • +
                  • + PhyloVision and Hotspot +
                    • +
                  • + Spatial Data and Hotspot +
                  • How To: Working with Seurat
                    • @@ -91,7 +97,7 @@
                    • - +
                      • @@ -105,7 +111,7 @@ -
                      +

                      How To: Loading 10x CellRanger Outputs

                      @@ -120,18 +126,19 @@

                      How To: Loading 10x CellRanger Outputs

                      VISION provides some convenience methods for loading gene expression data output from the 10x CellRanger pipeline.

                      The read_10x() and read_10x_h5() functions load count data from 10x and perform the ID conversion from Ensembl IDs to Gene Symbols. This is performed as most signature libraries refer to genes using symbols. The expression of genes whose symbols map to multiple Ensembl IDs are combined by summation. The resulting count matrix can then be scaled and input into VISION:

                      -
                      # Read in expression counts (Genes X Cells)
-counts <- read_10x(
-    expression = "outs/filtered_gene_bc_matrices/mm10/matrix.mtx",
-    genes = "outs/filtered_gene_bc_matrices/mm10/genes.tsv",
-    barcodes = "outs/filtered_gene_bc_matrices/mm10/barcodes.tsv"
-    )
+
                      +# Read in expression counts (Genes X Cells)
+counts <- read_10x(
+    expression = "outs/filtered_gene_bc_matrices/mm10/matrix.mtx",
+    genes = "outs/filtered_gene_bc_matrices/mm10/genes.tsv",
+    barcodes = "outs/filtered_gene_bc_matrices/mm10/barcodes.tsv"
+    )
 
 # Scale counts within a sample
-n.umi <- colSums(counts)
-scaled_counts <- t(t(counts) / n.umi) * median(n.umi)
+n.umi <- colSums(counts)
+scaled_counts <- t(t(counts) / n.umi) * median(n.umi)
 
-vis <- Vision(scaled_counts, signatures = c("data/h.all.v5.2.symbols.gmt"))
                      
+vis <- Vision(scaled_counts, signatures = c("data/h.all.v5.2.symbols.gmt"))

@@ -203,11 +209,11 @@

Contents

diff --git a/docs/reference/NormData.html b/docs/reference/NormData.html index 2a6f9526..fba316f1 100644 --- a/docs/reference/NormData.html +++ b/docs/reference/NormData.html @@ -90,7 +90,7 @@
@@ -208,11 +214,11 @@

Contents

diff --git a/docs/reference/ServerExpression.html b/docs/reference/ServerExpression.html index 460e1209..43aa04ef 100644 --- a/docs/reference/ServerExpression.html +++ b/docs/reference/ServerExpression.html @@ -90,7 +90,7 @@
@@ -194,11 +200,11 @@

Contents

diff --git a/docs/reference/ServerSigProjMatrix.html b/docs/reference/ServerSigProjMatrix.html index 4eb3a9ea..4738ed14 100644 --- a/docs/reference/ServerSigProjMatrix.html +++ b/docs/reference/ServerSigProjMatrix.html @@ -90,7 +90,7 @@
@@ -198,11 +204,11 @@

Contents

diff --git a/docs/reference/Signature.html b/docs/reference/Signature.html index 3171cfd4..a4d408fe 100644 --- a/docs/reference/Signature.html +++ b/docs/reference/Signature.html @@ -90,7 +90,7 @@
@@ -198,11 +204,11 @@

Contents

diff --git a/docs/reference/Trajectory.html b/docs/reference/Trajectory.html index 0cb0e53e..430f3ae3 100644 --- a/docs/reference/Trajectory.html +++ b/docs/reference/Trajectory.html @@ -90,7 +90,7 @@
@@ -187,11 +193,11 @@

Contents

diff --git a/docs/reference/TrajectoryProjection.html b/docs/reference/TrajectoryProjection.html index 5c7915af..4f2f5b34 100644 --- a/docs/reference/TrajectoryProjection.html +++ b/docs/reference/TrajectoryProjection.html @@ -90,7 +90,7 @@
@@ -198,11 +204,11 @@

Contents

diff --git a/docs/reference/VISION-class.html b/docs/reference/VISION-class.html index f4b26d0d..f0792284 100644 --- a/docs/reference/VISION-class.html +++ b/docs/reference/VISION-class.html @@ -93,7 +93,7 @@
@@ -364,19 +370,20 @@

Value

A VISION object

Examples

- 
if (FALSE) {
-expMat <- read.csv("expressionMatrix.csv", row.names=1)
-meta <- read.csv("metaData.csv", row.names=1)
+    
if (FALSE) {
+expMat <- read.csv("expressionMatrix.csv", row.names=1)
+meta <- read.csv("metaData.csv", row.names=1)
 
-sigs <- c("/path/to/signatures/msigdb_Hallmark.gmt",
+sigs <- c("/path/to/signatures/msigdb_Hallmark.gmt",
           "/path/to/signatures/Enrichr/ChEA_2015.txt"
-         )
+         )
 
 
-vis <- Vision(data = expMat,
-              signatures = sigs,
-              meta = meta)
-}

+vis <- Vision(data = expMat,
+              signatures = sigs,
+              meta = meta)
+}
+
- 
addLatentSpace(object, coordinates, name)
+ 
addLatentSpace(object, coordinates, name)

Arguments

@@ -194,11 +200,11 @@

Contents

diff --git a/docs/reference/addProjection-Vision-method.html b/docs/reference/addProjection-Vision-method.html index d4ae7500..81d235f6 100644 --- a/docs/reference/addProjection-Vision-method.html +++ b/docs/reference/addProjection-Vision-method.html @@ -95,7 +95,7 @@
@@ -196,22 +202,23 @@

Value

VISION object

Examples

- 
if (FALSE) {
+    
if (FALSE) {
 
 # First create the VISION object
-vis <- Vision(data = expMat, signatures = sigs)
+vis <- Vision(data = expMat, signatures = sigs)
 
 # Load and add an additional visualization
-my_umap <- read.csv("umap_results.csv")
-vis <- addProjection(vis, "UMAP", my_umap)
+my_umap <- read.csv("umap_results.csv")
+vis <- addProjection(vis, "UMAP", my_umap)
 
 # Run analysis
-vis <- analyze(vis)
+vis <- analyze(vis)
 
 # View results
-viewResults(vis)
+viewResults(vis)
 
-}

+}
+
- 
addSignatures(
-  object,
-  signatures,
-  min_signature_genes = 5,
-  sig_gene_threshold = 0.01
-)
+ 
addSignatures(
+  object,
+  signatures,
+  min_signature_genes = 5,
+  sig_gene_threshold = 0.01
+)

Arguments

@@ -207,11 +213,11 @@

Contents

diff --git a/docs/reference/addTSNE.html b/docs/reference/addTSNE.html index c37a37c0..43439071 100644 --- a/docs/reference/addTSNE.html +++ b/docs/reference/addTSNE.html @@ -90,7 +90,7 @@
@@ -199,11 +205,11 @@

Contents

diff --git a/docs/reference/addUMAP.html b/docs/reference/addUMAP.html index e9ed30e8..3dfb7f28 100644 --- a/docs/reference/addUMAP.html +++ b/docs/reference/addUMAP.html @@ -90,7 +90,7 @@
@@ -204,11 +210,11 @@

Contents

diff --git a/docs/reference/analyze-Vision-method.html b/docs/reference/analyze-Vision-method.html index e5f59727..6ceb4c18 100644 --- a/docs/reference/analyze-Vision-method.html +++ b/docs/reference/analyze-Vision-method.html @@ -91,7 +91,7 @@
@@ -183,14 +189,15 @@

Value

VISION object

Examples

- 
if (FALSE) {
+    
if (FALSE) {
 
-vis <- Vision(data = expMat, signatures = sigs)
+vis <- Vision(data = expMat, signatures = sigs)
 
-options(mc.cores=10) # Use 10 cores
-vis <- analyze(vis)
+options(mc.cores=10) # Use 10 cores
+vis <- analyze(vis)
 
-}

+}
+
- 
analyzeLocalCorrelations(object, tree = FALSE)
+ 
analyzeLocalCorrelations(object, tree = FALSE)

Arguments

@@ -192,11 +198,11 @@

Contents

diff --git a/docs/reference/analyzeTrajectoryCorrelations.html b/docs/reference/analyzeTrajectoryCorrelations.html index 32facc07..fb93ae78 100644 --- a/docs/reference/analyzeTrajectoryCorrelations.html +++ b/docs/reference/analyzeTrajectoryCorrelations.html @@ -93,7 +93,7 @@
@@ -192,11 +198,11 @@

Contents

diff --git a/docs/reference/annotateLatentComponents.html b/docs/reference/annotateLatentComponents.html index db0abab0..0f9a8601 100644 --- a/docs/reference/annotateLatentComponents.html +++ b/docs/reference/annotateLatentComponents.html @@ -90,7 +90,7 @@
@@ -186,11 +192,11 @@

Contents

diff --git a/docs/reference/applyFilters.html b/docs/reference/applyFilters.html index f442cc3c..ee5f35a2 100644 --- a/docs/reference/applyFilters.html +++ b/docs/reference/applyFilters.html @@ -90,7 +90,7 @@
@@ -198,11 +204,11 @@

Contents

diff --git a/docs/reference/applyICA.html b/docs/reference/applyICA.html index 61ac55e9..994556b4 100644 --- a/docs/reference/applyICA.html +++ b/docs/reference/applyICA.html @@ -90,7 +90,7 @@
@@ -186,11 +192,11 @@

Contents

diff --git a/docs/reference/applyISOMap.html b/docs/reference/applyISOMap.html index b013cb73..fdf3afd4 100644 --- a/docs/reference/applyISOMap.html +++ b/docs/reference/applyISOMap.html @@ -90,7 +90,7 @@
@@ -186,11 +192,11 @@

Contents

diff --git a/docs/reference/applyMicroClustering.html b/docs/reference/applyMicroClustering.html index e88f30d7..c6f579eb 100644 --- a/docs/reference/applyMicroClustering.html +++ b/docs/reference/applyMicroClustering.html @@ -90,7 +90,7 @@
@@ -228,11 +234,11 @@

Contents

diff --git a/docs/reference/applyPCA.html b/docs/reference/applyPCA.html index 4fa2f876..3ccdb301 100644 --- a/docs/reference/applyPCA.html +++ b/docs/reference/applyPCA.html @@ -90,7 +90,7 @@
@@ -192,11 +198,11 @@

Contents

diff --git a/docs/reference/applyPermutationWPCA.html b/docs/reference/applyPermutationWPCA.html index 0e5e5d91..a73b3e12 100644 --- a/docs/reference/applyPermutationWPCA.html +++ b/docs/reference/applyPermutationWPCA.html @@ -90,7 +90,7 @@
@@ -204,11 +210,11 @@

Contents

diff --git a/docs/reference/applyRBFPCA.html b/docs/reference/applyRBFPCA.html index c0edab8f..863d89b7 100644 --- a/docs/reference/applyRBFPCA.html +++ b/docs/reference/applyRBFPCA.html @@ -90,7 +90,7 @@
@@ -186,11 +192,11 @@

Contents

diff --git a/docs/reference/applySimplePPT.html b/docs/reference/applySimplePPT.html index 239ee442..f9650f19 100644 --- a/docs/reference/applySimplePPT.html +++ b/docs/reference/applySimplePPT.html @@ -90,7 +90,7 @@
@@ -227,11 +233,11 @@

Contents

diff --git a/docs/reference/applySpectralEmbedding.html b/docs/reference/applySpectralEmbedding.html index 169fb92e..33be6ced 100644 --- a/docs/reference/applySpectralEmbedding.html +++ b/docs/reference/applySpectralEmbedding.html @@ -90,7 +90,7 @@
@@ -186,11 +192,11 @@

Contents

diff --git a/docs/reference/applyUMAP.html b/docs/reference/applyUMAP.html index ca47e3e3..37e4c8d3 100644 --- a/docs/reference/applyUMAP.html +++ b/docs/reference/applyUMAP.html @@ -90,7 +90,7 @@
@@ -190,11 +196,11 @@

Contents

diff --git a/docs/reference/applytSNE10.html b/docs/reference/applytSNE10.html index c26dfe74..b4c7d0fe 100644 --- a/docs/reference/applytSNE10.html +++ b/docs/reference/applytSNE10.html @@ -90,7 +90,7 @@
@@ -186,11 +192,11 @@

Contents

diff --git a/docs/reference/applytSNE30.html b/docs/reference/applytSNE30.html index b1e45351..9ca37184 100644 --- a/docs/reference/applytSNE30.html +++ b/docs/reference/applytSNE30.html @@ -90,7 +90,7 @@
@@ -186,11 +192,11 @@

Contents

diff --git a/docs/reference/batchSigEvalNorm.html b/docs/reference/batchSigEvalNorm.html index b36fc1c9..2ac753f1 100644 --- a/docs/reference/batchSigEvalNorm.html +++ b/docs/reference/batchSigEvalNorm.html @@ -91,7 +91,7 @@
@@ -192,11 +198,11 @@

Contents

diff --git a/docs/reference/batchify.html b/docs/reference/batchify.html index d332f181..d44f8941 100644 --- a/docs/reference/batchify.html +++ b/docs/reference/batchify.html @@ -92,7 +92,7 @@
@@ -197,11 +203,11 @@

Contents

diff --git a/docs/reference/calcInterEdgeDistMat.html b/docs/reference/calcInterEdgeDistMat.html index 169b4d9d..8d5722f6 100644 --- a/docs/reference/calcInterEdgeDistMat.html +++ b/docs/reference/calcInterEdgeDistMat.html @@ -90,7 +90,7 @@
@@ -196,11 +202,11 @@

Contents

diff --git a/docs/reference/calcIntraEdgeDistMat.html b/docs/reference/calcIntraEdgeDistMat.html index abacc5c8..862ff3b3 100644 --- a/docs/reference/calcIntraEdgeDistMat.html +++ b/docs/reference/calcIntraEdgeDistMat.html @@ -90,7 +90,7 @@
@@ -190,11 +196,11 @@

Contents

diff --git a/docs/reference/calcSignatureScores.html b/docs/reference/calcSignatureScores.html index f3a4ba8c..aacbd16b 100644 --- a/docs/reference/calcSignatureScores.html +++ b/docs/reference/calcSignatureScores.html @@ -91,7 +91,7 @@
@@ -201,11 +207,11 @@

Contents

diff --git a/docs/reference/calculateTrajectoryDistances.html b/docs/reference/calculateTrajectoryDistances.html index 305662a8..60a74bc5 100644 --- a/docs/reference/calculateTrajectoryDistances.html +++ b/docs/reference/calculateTrajectoryDistances.html @@ -90,7 +90,7 @@
@@ -198,11 +204,11 @@

Contents

diff --git a/docs/reference/clipBottom.html b/docs/reference/clipBottom.html index b4f09253..edaf30bf 100644 --- a/docs/reference/clipBottom.html +++ b/docs/reference/clipBottom.html @@ -90,7 +90,7 @@
@@ -190,11 +196,11 @@

Contents

diff --git a/docs/reference/clusterCells.html b/docs/reference/clusterCells.html index c8e61a43..1e51f6db 100644 --- a/docs/reference/clusterCells.html +++ b/docs/reference/clusterCells.html @@ -90,7 +90,7 @@
@@ -186,11 +192,11 @@

Contents

diff --git a/docs/reference/clusterSigScores.html b/docs/reference/clusterSigScores.html index 25ca1429..046e1a8e 100644 --- a/docs/reference/clusterSigScores.html +++ b/docs/reference/clusterSigScores.html @@ -90,7 +90,7 @@
@@ -190,11 +196,11 @@

Contents

diff --git a/docs/reference/clusterSignatures.html b/docs/reference/clusterSignatures.html index 4ea14ea0..19119582 100644 --- a/docs/reference/clusterSignatures.html +++ b/docs/reference/clusterSignatures.html @@ -90,7 +90,7 @@
@@ -202,11 +208,11 @@

Contents

diff --git a/docs/reference/colNormalization.html b/docs/reference/colNormalization.html index 19427e26..713c35ed 100644 --- a/docs/reference/colNormalization.html +++ b/docs/reference/colNormalization.html @@ -90,7 +90,7 @@
@@ -186,11 +192,11 @@

Contents

diff --git a/docs/reference/colRankNormalization.html b/docs/reference/colRankNormalization.html index ff2b0ee7..a2f0a6e4 100644 --- a/docs/reference/colRankNormalization.html +++ b/docs/reference/colRankNormalization.html @@ -90,7 +90,7 @@
@@ -186,11 +192,11 @@

Contents

diff --git a/docs/reference/colVarsSp.html b/docs/reference/colVarsSp.html index 8a81d72d..bb8af4e1 100644 --- a/docs/reference/colVarsSp.html +++ b/docs/reference/colVarsSp.html @@ -90,7 +90,7 @@
@@ -186,11 +192,11 @@

Contents

diff --git a/docs/reference/computeKNNWeights-Trajectory-method.html b/docs/reference/computeKNNWeights-Trajectory-method.html index 35d61adb..7b7a3ba0 100644 --- a/docs/reference/computeKNNWeights-Trajectory-method.html +++ b/docs/reference/computeKNNWeights-Trajectory-method.html @@ -90,7 +90,7 @@
@@ -195,11 +201,11 @@

Contents

diff --git a/docs/reference/computeKNNWeights-matrix-method.html b/docs/reference/computeKNNWeights-matrix-method.html index fa4d215f..e974ea79 100644 --- a/docs/reference/computeKNNWeights-matrix-method.html +++ b/docs/reference/computeKNNWeights-matrix-method.html @@ -90,7 +90,7 @@
@@ -195,11 +201,11 @@

Contents

diff --git a/docs/reference/computeLatentSpace.html b/docs/reference/computeLatentSpace.html index 1a38c56e..8459df10 100644 --- a/docs/reference/computeLatentSpace.html +++ b/docs/reference/computeLatentSpace.html @@ -90,7 +90,7 @@
@@ -222,11 +228,11 @@

Contents

diff --git a/docs/reference/computeProjectionGenes.html b/docs/reference/computeProjectionGenes.html index 0a76e9cd..e8b187b2 100644 --- a/docs/reference/computeProjectionGenes.html +++ b/docs/reference/computeProjectionGenes.html @@ -90,7 +90,7 @@
@@ -212,11 +218,11 @@

Contents

diff --git a/docs/reference/convertGeneIds.html b/docs/reference/convertGeneIds.html index e599c5d1..168a71a5 100644 --- a/docs/reference/convertGeneIds.html +++ b/docs/reference/convertGeneIds.html @@ -91,7 +91,7 @@
@@ -189,14 +195,16 @@

Details

Examples

-exp <- matrix(c(1, 1, 1, 2, 2, 2, 3, 3, 3), nrow=3)
-colnames(exp) <- c("Cell1", "Cell2", "Cell3")
-print(exp)
+exp <- matrix(c(1, 1, 1, 2, 2, 2, 3, 3, 3), nrow=3)
+colnames(exp) <- c("Cell1", "Cell2", "Cell3")
+print(exp)
+
+newIds <- c("GeneA", "GeneA", "GeneB")
 
-newIds <- c("GeneA", "GeneA", "GeneB")
+result <- convertGeneIds(exp, newIds)
+print(result)
 
-result <- convertGeneIds(exp, newIds)
-print(result)
+ - 
coordinatesToJSON(p)
+ 
coordinatesToJSON(p)

Arguments

@@ -186,11 +192,11 @@

Contents

diff --git a/docs/reference/createGeneSignature.html b/docs/reference/createGeneSignature.html index 925221c6..9a8e106a 100644 --- a/docs/reference/createGeneSignature.html +++ b/docs/reference/createGeneSignature.html @@ -93,7 +93,7 @@
@@ -193,21 +199,22 @@

Value

a Signature object

Examples

- 
if (FALSE) {
-sig1 <- createGeneSignature(
-           name = "CD8 Markers",
-           sigData = c(CD8A=1, CD8B=1, GZMK=1, GZMB=1,
-                       GZMH=1, GZMA=1, GNLY=1, DUSP2=1,
-                       EOMES=1, TBX21=1, PRMD1=1, PRF1=1,
-                       IFNG=1)
-       )
-
-cc_sigs <- "path/to/cell_cycle.gmt"
-
-sigs <- c(sig1, cc_sigs)
-
-vis <- Vision(data = expMat, signatures = sigs)
-}
+ 
if (FALSE) {
+sig1 <- createGeneSignature(
+           name = "CD8 Markers",
+           sigData = c(CD8A=1, CD8B=1, GZMK=1, GZMB=1,
+                       GZMH=1, GZMA=1, GNLY=1, DUSP2=1,
+                       EOMES=1, TBX21=1, PRMD1=1, PRF1=1,
+                       IFNG=1)
+       )
+
+cc_sigs <- "path/to/cell_cycle.gmt"
+
+sigs <- c(sig1, cc_sigs)
+
+vis <- Vision(data = expMat, signatures = sigs)
+}
+
- 
createTrajectoryMetaData(trajectory)
+ 
createTrajectoryMetaData(trajectory)

Arguments

@@ -188,11 +194,11 @@

Contents

diff --git a/docs/reference/dot-colNormHelper.html b/docs/reference/dot-colNormHelper.html index b4cfead3..2220d83c 100644 --- a/docs/reference/dot-colNormHelper.html +++ b/docs/reference/dot-colNormHelper.html @@ -90,7 +90,7 @@
@@ -194,11 +200,11 @@

Contents

diff --git a/docs/reference/evalSigGeneImportance.html b/docs/reference/evalSigGeneImportance.html index d97740c6..9c1ce824 100644 --- a/docs/reference/evalSigGeneImportance.html +++ b/docs/reference/evalSigGeneImportance.html @@ -92,7 +92,7 @@
@@ -199,11 +205,11 @@

Contents

diff --git a/docs/reference/evalSigGeneImportanceSparse.html b/docs/reference/evalSigGeneImportanceSparse.html index 1f3685a8..273aa9fc 100644 --- a/docs/reference/evalSigGeneImportanceSparse.html +++ b/docs/reference/evalSigGeneImportanceSparse.html @@ -92,7 +92,7 @@
@@ -207,11 +213,11 @@

Contents

diff --git a/docs/reference/fbConsistencyScores.html b/docs/reference/fbConsistencyScores.html index 5bcd482e..7c55874a 100644 --- a/docs/reference/fbConsistencyScores.html +++ b/docs/reference/fbConsistencyScores.html @@ -90,7 +90,7 @@
@@ -191,11 +197,11 @@

Contents

diff --git a/docs/reference/filterGenesFano.html b/docs/reference/filterGenesFano.html index 5ead853c..a181f47c 100644 --- a/docs/reference/filterGenesFano.html +++ b/docs/reference/filterGenesFano.html @@ -90,7 +90,7 @@
@@ -194,11 +200,11 @@

Contents

diff --git a/docs/reference/filterGenesNovar.html b/docs/reference/filterGenesNovar.html index 22918355..eb84b18d 100644 --- a/docs/reference/filterGenesNovar.html +++ b/docs/reference/filterGenesNovar.html @@ -96,7 +96,7 @@
@@ -196,11 +202,11 @@

Contents

diff --git a/docs/reference/filterGenesThreshold.html b/docs/reference/filterGenesThreshold.html index c563c8f7..98167923 100644 --- a/docs/reference/filterGenesThreshold.html +++ b/docs/reference/filterGenesThreshold.html @@ -90,7 +90,7 @@
@@ -190,11 +196,11 @@

Contents

diff --git a/docs/reference/find_knn_parallel.html b/docs/reference/find_knn_parallel.html index ef2728be..bbadbb38 100644 --- a/docs/reference/find_knn_parallel.html +++ b/docs/reference/find_knn_parallel.html @@ -92,7 +92,7 @@
@@ -196,11 +202,11 @@

Contents

diff --git a/docs/reference/fitTree.html b/docs/reference/fitTree.html index 8b6b1fff..ae22c586 100644 --- a/docs/reference/fitTree.html +++ b/docs/reference/fitTree.html @@ -90,7 +90,7 @@
@@ -213,11 +219,11 @@

Contents

diff --git a/docs/reference/geary_sig_v_proj.html b/docs/reference/geary_sig_v_proj.html index ca1f7cfd..83280cee 100644 --- a/docs/reference/geary_sig_v_proj.html +++ b/docs/reference/geary_sig_v_proj.html @@ -90,7 +90,7 @@
@@ -195,11 +201,11 @@

Contents

diff --git a/docs/reference/generatePermutationNull.html b/docs/reference/generatePermutationNull.html index 762ed737..07aa63f8 100644 --- a/docs/reference/generatePermutationNull.html +++ b/docs/reference/generatePermutationNull.html @@ -90,7 +90,7 @@
@@ -199,11 +205,11 @@

Contents

diff --git a/docs/reference/generateProjections.html b/docs/reference/generateProjections.html index 862b3c06..8d168d2d 100644 --- a/docs/reference/generateProjections.html +++ b/docs/reference/generateProjections.html @@ -91,7 +91,7 @@
@@ -188,11 +194,11 @@

Contents

diff --git a/docs/reference/generateProjectionsInner.html b/docs/reference/generateProjectionsInner.html index 60ef812f..5c8d0575 100644 --- a/docs/reference/generateProjectionsInner.html +++ b/docs/reference/generateProjectionsInner.html @@ -90,7 +90,7 @@
@@ -208,11 +214,11 @@

Contents

diff --git a/docs/reference/generateTrajectoryProjections.html b/docs/reference/generateTrajectoryProjections.html index 22849658..7234223f 100644 --- a/docs/reference/generateTrajectoryProjections.html +++ b/docs/reference/generateTrajectoryProjections.html @@ -91,7 +91,7 @@
@@ -188,11 +194,11 @@

Contents

diff --git a/docs/reference/getLatentSpace.html b/docs/reference/getLatentSpace.html index 8a54d3ad..111765e7 100644 --- a/docs/reference/getLatentSpace.html +++ b/docs/reference/getLatentSpace.html @@ -91,7 +91,7 @@
@@ -193,11 +199,11 @@

Contents

diff --git a/docs/reference/getLatentTrajectory.html b/docs/reference/getLatentTrajectory.html index 62976cbb..37984ecb 100644 --- a/docs/reference/getLatentTrajectory.html +++ b/docs/reference/getLatentTrajectory.html @@ -91,7 +91,7 @@
@@ -183,12 +189,12 @@

Details instead

Examples

- 
if (FALSE) {
+    
if (FALSE) {
 
-trajectory <- getLatentTrajectory(vis)
+trajectory <- getLatentTrajectory(vis)
 
 # MxM connectivity for network milestones
-trajectory@adjMat
+trajectory@adjMat
 
 # data.frame with the position of cells between milestones
 # Columns are:
@@ -196,9 +202,10 @@ 
Examp
 #    from (milestone)
 #    to (milestone)
 #    position (0 to 1)
-trajectory@progressions
+trajectory@progressions
 
-}

+}
+
- 
getMSE(C, X)
+ 
getMSE(C, X)

Arguments

@@ -190,11 +196,11 @@

Contents

diff --git a/docs/reference/getMetaAutocorrelation.html b/docs/reference/getMetaAutocorrelation.html index 24b95106..0948cb0f 100644 --- a/docs/reference/getMetaAutocorrelation.html +++ b/docs/reference/getMetaAutocorrelation.html @@ -90,7 +90,7 @@
@@ -191,11 +197,11 @@

Contents

diff --git a/docs/reference/getMetaDifferential.html b/docs/reference/getMetaDifferential.html index d9b4b576..44bb2db2 100644 --- a/docs/reference/getMetaDifferential.html +++ b/docs/reference/getMetaDifferential.html @@ -91,7 +91,7 @@
@@ -196,11 +202,11 @@

Contents

diff --git a/docs/reference/getNormalizedCopy.html b/docs/reference/getNormalizedCopy.html index 7d09cc66..b6bf8d96 100644 --- a/docs/reference/getNormalizedCopy.html +++ b/docs/reference/getNormalizedCopy.html @@ -90,7 +90,7 @@
@@ -190,11 +196,11 @@

Contents

diff --git a/docs/reference/getNormalizedCopySparse.html b/docs/reference/getNormalizedCopySparse.html index 9a9c48dd..6f7985fa 100644 --- a/docs/reference/getNormalizedCopySparse.html +++ b/docs/reference/getNormalizedCopySparse.html @@ -90,7 +90,7 @@
@@ -190,11 +196,11 @@

Contents

diff --git a/docs/reference/getParam.html b/docs/reference/getParam.html index 94757c5e..633a8509 100644 --- a/docs/reference/getParam.html +++ b/docs/reference/getParam.html @@ -90,7 +90,7 @@
@@ -194,11 +200,11 @@

Contents

diff --git a/docs/reference/getProjections.html b/docs/reference/getProjections.html index 6f34c0f5..5f1ad7af 100644 --- a/docs/reference/getProjections.html +++ b/docs/reference/getProjections.html @@ -91,7 +91,7 @@
@@ -179,20 +185,21 @@

Value

List of matrix (Cells x 2)

Examples

- 
if (FALSE) {
+    
if (FALSE) {
 
 # After running 'analyze'
 # Retrieve tSNE30 (tSNE with perplexity 30) and plot it
 
-tsne <- getProjections(vis)[["tSNE30"]]
+tsne <- getProjections(vis)[["tSNE30"]]
 
-plot(tsne[, 1], tsne[, 2])
+plot(tsne[, 1], tsne[, 2])
 
 # To see the names of available projections, just run:
 
-names(getProjections(vis))
+names(getProjections(vis))
 
-}

+}
+
# S4 method for Vision
-getSelections(object)
+getSelections(object)

Arguments

@@ -180,18 +186,19 @@

Details

This method allows you to retrieve saved selections later in R for downstream analyses

Note: In order for selections to correctly save when launching the report, the report must be run by storing the results back into the object.

-

E.g.

vis &lt;- viewResults(vis)

and not

viewResults(vis)
+

E.g.

vis <- viewResults(vis)

and not

viewResults(vis)

Examples

- 
if (FALSE) {
+    
if (FALSE) {
 
-vis <- viewResults(vis)  # Selections saved while viewing results
+vis <- viewResults(vis)  # Selections saved while viewing results
 
 # Retrieve cell IDs for a selection group named 'interesting cells'
-interestingCells <- getSelections(vis)[['interesting cells']]
+interestingCells <- getSelections(vis)[['interesting cells']]
 
-}

+}
+
# S4 method for Vision
-getSignatureAutocorrelation(object)
+getSignatureAutocorrelation(object)

Arguments

@@ -191,11 +197,11 @@

Contents

diff --git a/docs/reference/getSignatureDifferential.html b/docs/reference/getSignatureDifferential.html index 27c697e5..a8987646 100644 --- a/docs/reference/getSignatureDifferential.html +++ b/docs/reference/getSignatureDifferential.html @@ -91,7 +91,7 @@
@@ -195,11 +201,11 @@

Contents

diff --git a/docs/reference/getSignatureScores.html b/docs/reference/getSignatureScores.html index 193e871d..e9fedfa1 100644 --- a/docs/reference/getSignatureScores.html +++ b/docs/reference/getSignatureScores.html @@ -90,7 +90,7 @@
@@ -187,11 +193,11 @@

Contents

diff --git a/docs/reference/hasUnnormalizedData.html b/docs/reference/hasUnnormalizedData.html index abe79387..5badd48c 100644 --- a/docs/reference/hasUnnormalizedData.html +++ b/docs/reference/hasUnnormalizedData.html @@ -90,7 +90,7 @@
@@ -186,11 +192,11 @@

Contents

diff --git a/docs/reference/ilog1p.html b/docs/reference/ilog1p.html index 1473b053..0733f500 100644 --- a/docs/reference/ilog1p.html +++ b/docs/reference/ilog1p.html @@ -91,7 +91,7 @@
@@ -191,11 +197,11 @@

Contents

diff --git a/docs/reference/index.html b/docs/reference/index.html index 6aa885c7..7893cbb1 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -89,7 +89,7 @@ + + + + + + + + + + + + + + + + + + + + - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

Aggregate meta-data for cells in pools
+

PhyloVision

+

+
+

Hotspot

+

+
@@ -366,11 +398,11 @@

Contents

-

Developed by Matt Jones, David Detomaso, Tal Ashuach.

+

Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

-

Site built with pkgdown 1.5.1.

+

Site built with pkgdown 1.6.1.

diff --git a/docs/reference/innerEvalSignatureBatchNorm.html b/docs/reference/innerEvalSignatureBatchNorm.html index ab32a546..d5f2bde7 100644 --- a/docs/reference/innerEvalSignatureBatchNorm.html +++ b/docs/reference/innerEvalSignatureBatchNorm.html @@ -90,7 +90,7 @@
  • - +
    • @@ -116,6 +116,12 @@
  • Incorporating a Trajectory Model
    • +
  • + PhyloVision and Hotspot +
    • +
  • + Spatial Data and Hotspot +
  • How To: Working with Seurat
    • @@ -134,7 +140,7 @@
    • - +
      • @@ -160,7 +166,7 @@

      Used in inner loop of batchSigEvalNorm

      Computes signature scores without inflating the genes/cells matrix

      - 
      innerEvalSignatureBatchNorm(normData, sigs)
      + 
      innerEvalSignatureBatchNorm(normData, sigs)

      Arguments

      @@ -190,11 +196,11 @@

      Contents

      -

      Developed by Matt Jones, David Detomaso, Tal Ashuach.

      +

      Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

      -

      Site built with pkgdown 1.5.1.

      +

      Site built with pkgdown 1.6.1.

      diff --git a/docs/reference/launchServer.html b/docs/reference/launchServer.html index dad2e80b..1d5980e2 100644 --- a/docs/reference/launchServer.html +++ b/docs/reference/launchServer.html @@ -90,7 +90,7 @@
      @@ -200,11 +206,11 @@

      Contents

      -

      Developed by Matt Jones, David Detomaso, Tal Ashuach.

      +

      Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

      -

      Site built with pkgdown 1.5.1.

      +

      Site built with pkgdown 1.6.1.

      diff --git a/docs/reference/louvainCluster.html b/docs/reference/louvainCluster.html index 4b72ba73..a1c8ccdc 100644 --- a/docs/reference/louvainCluster.html +++ b/docs/reference/louvainCluster.html @@ -90,7 +90,7 @@
      @@ -192,11 +198,11 @@

      Contents

      -

      Developed by Matt Jones, David Detomaso, Tal Ashuach.

      +

      Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

      -

      Site built with pkgdown 1.5.1.

      +

      Site built with pkgdown 1.6.1.

      diff --git a/docs/reference/matLog2.html b/docs/reference/matLog2.html index 45a297d9..384241f1 100644 --- a/docs/reference/matLog2.html +++ b/docs/reference/matLog2.html @@ -91,7 +91,7 @@
      @@ -200,11 +206,11 @@

      Contents

      -

      Developed by Matt Jones, David Detomaso, Tal Ashuach.

      +

      Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

      -

      Site built with pkgdown 1.5.1.

      +

      Site built with pkgdown 1.6.1.

      diff --git a/docs/reference/matrix_chisq.html b/docs/reference/matrix_chisq.html index e4b3cd63..c9a1c64b 100644 --- a/docs/reference/matrix_chisq.html +++ b/docs/reference/matrix_chisq.html @@ -91,7 +91,7 @@
      @@ -193,11 +199,11 @@

      Contents

      -

      Developed by Matt Jones, David Detomaso, Tal Ashuach.

      +

      Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

      -

      Site built with pkgdown 1.5.1.

      +

      Site built with pkgdown 1.6.1.

      diff --git a/docs/reference/matrix_wilcox.html b/docs/reference/matrix_wilcox.html index 1992f176..02153d73 100644 --- a/docs/reference/matrix_wilcox.html +++ b/docs/reference/matrix_wilcox.html @@ -91,7 +91,7 @@
      @@ -201,11 +207,11 @@

      Contents

      -

      Developed by Matt Jones, David Detomaso, Tal Ashuach.

      +

      Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

      -

      Site built with pkgdown 1.5.1.

      +

      Site built with pkgdown 1.6.1.

      diff --git a/docs/reference/matrix_wilcox_cpp.html b/docs/reference/matrix_wilcox_cpp.html index 4e2c126a..43c94643 100644 --- a/docs/reference/matrix_wilcox_cpp.html +++ b/docs/reference/matrix_wilcox_cpp.html @@ -91,7 +91,7 @@
      @@ -210,11 +216,11 @@

      Contents

      -

      Developed by Matt Jones, David Detomaso, Tal Ashuach.

      +

      Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

      -

      Site built with pkgdown 1.5.1.

      +

      Site built with pkgdown 1.6.1.

      diff --git a/docs/reference/noNormalization.html b/docs/reference/noNormalization.html index b5bdfc6d..5190ac71 100644 --- a/docs/reference/noNormalization.html +++ b/docs/reference/noNormalization.html @@ -90,7 +90,7 @@
      @@ -186,11 +192,11 @@

      Contents

      -

      Developed by Matt Jones, David Detomaso, Tal Ashuach.

      +

      Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

      -

      Site built with pkgdown 1.5.1.

      +

      Site built with pkgdown 1.6.1.

      diff --git a/docs/reference/pearsonCorrToJSON.html b/docs/reference/pearsonCorrToJSON.html index 0d4e4b35..a3eb2667 100644 --- a/docs/reference/pearsonCorrToJSON.html +++ b/docs/reference/pearsonCorrToJSON.html @@ -90,7 +90,7 @@
      @@ -190,11 +196,11 @@

      Contents

      -

      Developed by Matt Jones, David Detomaso, Tal Ashuach.

      +

      Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

      -

      Site built with pkgdown 1.5.1.

      +

      Site built with pkgdown 1.6.1.

      diff --git a/docs/reference/poolCells.html b/docs/reference/poolCells.html index 751be96f..1a400e00 100644 --- a/docs/reference/poolCells.html +++ b/docs/reference/poolCells.html @@ -93,7 +93,7 @@
      @@ -195,11 +201,11 @@

      Contents

      -

      Developed by Matt Jones, David Detomaso, Tal Ashuach.

      +

      Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

      -

      Site built with pkgdown 1.5.1.

      +

      Site built with pkgdown 1.6.1.

      diff --git a/docs/reference/poolMatrixCols.html b/docs/reference/poolMatrixCols.html index 6421dbdf..43f19245 100644 --- a/docs/reference/poolMatrixCols.html +++ b/docs/reference/poolMatrixCols.html @@ -90,7 +90,7 @@
      @@ -196,11 +202,11 @@

      Contents

      -

      Developed by Matt Jones, David Detomaso, Tal Ashuach.

      +

      Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

      -

      Site built with pkgdown 1.5.1.

      +

      Site built with pkgdown 1.6.1.

      diff --git a/docs/reference/poolMatrixCols_Inner.html b/docs/reference/poolMatrixCols_Inner.html index 64bb4d2a..a87c4e67 100644 --- a/docs/reference/poolMatrixCols_Inner.html +++ b/docs/reference/poolMatrixCols_Inner.html @@ -90,7 +90,7 @@
      @@ -190,11 +196,11 @@

      Contents

      -

      Developed by Matt Jones, David Detomaso, Tal Ashuach.

      +

      Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

      -

      Site built with pkgdown 1.5.1.

      +

      Site built with pkgdown 1.6.1.

      diff --git a/docs/reference/poolMatrixRows.html b/docs/reference/poolMatrixRows.html index 51b9a171..2df19d0a 100644 --- a/docs/reference/poolMatrixRows.html +++ b/docs/reference/poolMatrixRows.html @@ -90,7 +90,7 @@
      @@ -195,11 +201,11 @@

      Contents

      -

      Developed by Matt Jones, David Detomaso, Tal Ashuach.

      +

      Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

      -

      Site built with pkgdown 1.5.1.

      +

      Site built with pkgdown 1.6.1.

      diff --git a/docs/reference/poolMetaData.html b/docs/reference/poolMetaData.html index 36d3cdd2..f9aeef5e 100644 --- a/docs/reference/poolMetaData.html +++ b/docs/reference/poolMetaData.html @@ -91,7 +91,7 @@
      @@ -203,11 +209,11 @@

      Contents

      -

      Developed by Matt Jones, David Detomaso, Tal Ashuach.

      +

      Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

      -

      Site built with pkgdown 1.5.1.

      +

      Site built with pkgdown 1.6.1.

      diff --git a/docs/reference/processSignatures.html b/docs/reference/processSignatures.html index 71d57992..bbd0c79d 100644 --- a/docs/reference/processSignatures.html +++ b/docs/reference/processSignatures.html @@ -91,7 +91,7 @@
      @@ -202,11 +208,11 @@

      Contents

      -

      Developed by Matt Jones, David Detomaso, Tal Ashuach.

      +

      Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

      -

      Site built with pkgdown 1.5.1.

      +

      Site built with pkgdown 1.6.1.

      diff --git a/docs/reference/projectOnTree.html b/docs/reference/projectOnTree.html index 069da694..11ba8fcc 100644 --- a/docs/reference/projectOnTree.html +++ b/docs/reference/projectOnTree.html @@ -90,7 +90,7 @@
      @@ -206,11 +212,11 @@

      Contents

      -

      Developed by Matt Jones, David Detomaso, Tal Ashuach.

      +

      Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

      -

      Site built with pkgdown 1.5.1.

      +

      Site built with pkgdown 1.6.1.

      diff --git a/docs/reference/readSignaturesInput.html b/docs/reference/readSignaturesInput.html index 705d32d3..f00cc344 100644 --- a/docs/reference/readSignaturesInput.html +++ b/docs/reference/readSignaturesInput.html @@ -90,7 +90,7 @@
      @@ -186,11 +192,11 @@

      Contents

      -

      Developed by Matt Jones, David Detomaso, Tal Ashuach.

      +

      Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

      -

      Site built with pkgdown 1.5.1.

      +

      Site built with pkgdown 1.6.1.

      diff --git a/docs/reference/read_10x.html b/docs/reference/read_10x.html index cd21025f..6c566c9c 100644 --- a/docs/reference/read_10x.html +++ b/docs/reference/read_10x.html @@ -90,7 +90,7 @@
      @@ -210,11 +216,11 @@

      Contents

      -

      Developed by Matt Jones, David Detomaso, Tal Ashuach.

      +

      Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

      -

      Site built with pkgdown 1.5.1.

      +

      Site built with pkgdown 1.6.1.

      diff --git a/docs/reference/read_10x_h5.html b/docs/reference/read_10x_h5.html index 94f89e8a..071046a3 100644 --- a/docs/reference/read_10x_h5.html +++ b/docs/reference/read_10x_h5.html @@ -90,7 +90,7 @@
      @@ -199,11 +205,11 @@

      Contents

      -

      Developed by Matt Jones, David Detomaso, Tal Ashuach.

      +

      Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

      -

      Site built with pkgdown 1.5.1.

      +

      Site built with pkgdown 1.6.1.

      diff --git a/docs/reference/read_10x_h5_v2.html b/docs/reference/read_10x_h5_v2.html index 1c74ba27..3ae0377e 100644 --- a/docs/reference/read_10x_h5_v2.html +++ b/docs/reference/read_10x_h5_v2.html @@ -90,7 +90,7 @@
      @@ -195,11 +201,11 @@

      Contents

      -

      Developed by Matt Jones, David Detomaso, Tal Ashuach.

      +

      Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

      -

      Site built with pkgdown 1.5.1.

      +

      Site built with pkgdown 1.6.1.

      diff --git a/docs/reference/read_10x_h5_v3.html b/docs/reference/read_10x_h5_v3.html index 52452fba..135adac9 100644 --- a/docs/reference/read_10x_h5_v3.html +++ b/docs/reference/read_10x_h5_v3.html @@ -90,7 +90,7 @@
      @@ -197,11 +203,11 @@

      Contents

      -

      Developed by Matt Jones, David Detomaso, Tal Ashuach.

      +

      Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

      -

      Site built with pkgdown 1.5.1.

      +

      Site built with pkgdown 1.6.1.

      diff --git a/docs/reference/readjust_clusters.html b/docs/reference/readjust_clusters.html index 3d3094cd..3b316ec4 100644 --- a/docs/reference/readjust_clusters.html +++ b/docs/reference/readjust_clusters.html @@ -91,7 +91,7 @@
      @@ -200,11 +206,11 @@

      Contents

      -

      Developed by Matt Jones, David Detomaso, Tal Ashuach.

      +

      Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

      -

      Site built with pkgdown 1.5.1.

      +

      Site built with pkgdown 1.6.1.

      diff --git a/docs/reference/registerMethods.html b/docs/reference/registerMethods.html index 04dedf6a..2d30cca7 100644 --- a/docs/reference/registerMethods.html +++ b/docs/reference/registerMethods.html @@ -90,7 +90,7 @@
      @@ -190,11 +196,11 @@

      Contents

      -

      Developed by Matt Jones, David Detomaso, Tal Ashuach.

      +

      Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

      -

      Site built with pkgdown 1.5.1.

      +

      Site built with pkgdown 1.6.1.

      diff --git a/docs/reference/rowAndColNormalization.html b/docs/reference/rowAndColNormalization.html index 5b77d4cc..7246ed7a 100644 --- a/docs/reference/rowAndColNormalization.html +++ b/docs/reference/rowAndColNormalization.html @@ -90,7 +90,7 @@
      @@ -186,11 +192,11 @@

      Contents

      -

      Developed by Matt Jones, David Detomaso, Tal Ashuach.

      +

      Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

      -

      Site built with pkgdown 1.5.1.

      +

      Site built with pkgdown 1.6.1.

      diff --git a/docs/reference/rowNormalization.html b/docs/reference/rowNormalization.html index 97f2107b..8b0137a2 100644 --- a/docs/reference/rowNormalization.html +++ b/docs/reference/rowNormalization.html @@ -90,7 +90,7 @@
      @@ -186,11 +192,11 @@

      Contents

      -

      Developed by Matt Jones, David Detomaso, Tal Ashuach.

      +

      Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

      -

      Site built with pkgdown 1.5.1.

      +

      Site built with pkgdown 1.6.1.

      diff --git a/docs/reference/rowVarsSp.html b/docs/reference/rowVarsSp.html index ec24ccce..3ab03830 100644 --- a/docs/reference/rowVarsSp.html +++ b/docs/reference/rowVarsSp.html @@ -90,7 +90,7 @@
      @@ -186,11 +192,11 @@

      Contents

      -

      Developed by Matt Jones, David Detomaso, Tal Ashuach.

      +

      Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

      -

      Site built with pkgdown 1.5.1.

      +

      Site built with pkgdown 1.6.1.

      diff --git a/docs/reference/saveAndViewResults-Vision-method.html b/docs/reference/saveAndViewResults-Vision-method.html index 8bf8bde6..71a7aa49 100644 --- a/docs/reference/saveAndViewResults-Vision-method.html +++ b/docs/reference/saveAndViewResults-Vision-method.html @@ -92,7 +92,7 @@
      @@ -216,15 +222,16 @@

      Details viewResults(vis)

      Examples

      - 
      if (FALSE) {
+    
      if (FALSE) {
 
-vis <- Vision(data = expMat, signatures = sigs)
+vis <- Vision(data = expMat, signatures = sigs)
 
-options(mc.cores=10) # Use 10 cores
-vis <- analyze(vis)
+options(mc.cores=10) # Use 10 cores
+vis <- analyze(vis)
 
-saveAndViewResults(vis, 'vision_results.rds') # Saves and launches dynamic output report
-}
      
+saveAndViewResults(vis, 'vision_results.rds') # Saves and launches dynamic output report
+}
+
      - 
      sigConsistencyScores(weights, sigScoresData, metaData, randomSigData, normExpr)
      + 
      sigConsistencyScores(weights, sigScoresData, metaData, randomSigData, normExpr)

      Arguments

      @@ -213,11 +219,11 @@

      Contents

      -

      Developed by Matt Jones, David Detomaso, Tal Ashuach.

      +

      Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

      -

      Site built with pkgdown 1.5.1.

      +

      Site built with pkgdown 1.6.1.

      diff --git a/docs/reference/sigProjMatrixToJSON.html b/docs/reference/sigProjMatrixToJSON.html index 7840182e..4a440880 100644 --- a/docs/reference/sigProjMatrixToJSON.html +++ b/docs/reference/sigProjMatrixToJSON.html @@ -90,7 +90,7 @@
      @@ -194,11 +200,11 @@

      Contents

      -

      Developed by Matt Jones, David Detomaso, Tal Ashuach.

      +

      Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

      -

      Site built with pkgdown 1.5.1.

      +

      Site built with pkgdown 1.6.1.

      diff --git a/docs/reference/sigScoresToJSON.html b/docs/reference/sigScoresToJSON.html index bf664c5d..51c719a8 100644 --- a/docs/reference/sigScoresToJSON.html +++ b/docs/reference/sigScoresToJSON.html @@ -90,7 +90,7 @@
      @@ -190,11 +196,11 @@

      Contents

      -

      Developed by Matt Jones, David Detomaso, Tal Ashuach.

      +

      Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

      -

      Site built with pkgdown 1.5.1.

      +

      Site built with pkgdown 1.6.1.

      diff --git a/docs/reference/signatureToJSON.html b/docs/reference/signatureToJSON.html index c3e5d14a..0ab81c9b 100644 --- a/docs/reference/signatureToJSON.html +++ b/docs/reference/signatureToJSON.html @@ -90,7 +90,7 @@
      @@ -190,11 +196,11 @@

      Contents

      -

      Developed by Matt Jones, David Detomaso, Tal Ashuach.

      +

      Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

      -

      Site built with pkgdown 1.5.1.

      +

      Site built with pkgdown 1.6.1.

      diff --git a/docs/reference/sigsToSparseMatrix.html b/docs/reference/sigsToSparseMatrix.html index 7ba0115f..aa880546 100644 --- a/docs/reference/sigsToSparseMatrix.html +++ b/docs/reference/sigsToSparseMatrix.html @@ -90,7 +90,7 @@
      @@ -190,11 +196,11 @@

      Contents

      -

      Developed by Matt Jones, David Detomaso, Tal Ashuach.

      +

      Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

      -

      Site built with pkgdown 1.5.1.

      +

      Site built with pkgdown 1.6.1.

      diff --git a/docs/reference/sigsVsProjection_n.html b/docs/reference/sigsVsProjection_n.html index c51f2d58..463f6d65 100644 --- a/docs/reference/sigsVsProjection_n.html +++ b/docs/reference/sigsVsProjection_n.html @@ -93,7 +93,7 @@
      @@ -222,11 +228,11 @@

      Contents

      -

      Developed by Matt Jones, David Detomaso, Tal Ashuach.

      +

      Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

      -

      Site built with pkgdown 1.5.1.

      +

      Site built with pkgdown 1.6.1.

      diff --git a/docs/reference/sigsVsProjection_pcf.html b/docs/reference/sigsVsProjection_pcf.html index 0146e4dc..6025e730 100644 --- a/docs/reference/sigsVsProjection_pcf.html +++ b/docs/reference/sigsVsProjection_pcf.html @@ -93,7 +93,7 @@
      @@ -204,11 +210,11 @@

      Contents

      -

      Developed by Matt Jones, David Detomaso, Tal Ashuach.

      +

      Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

      -

      Site built with pkgdown 1.5.1.

      +

      Site built with pkgdown 1.6.1.

      diff --git a/docs/reference/sigsVsProjection_pcn.html b/docs/reference/sigsVsProjection_pcn.html index 20fbbd44..f29093a1 100644 --- a/docs/reference/sigsVsProjection_pcn.html +++ b/docs/reference/sigsVsProjection_pcn.html @@ -93,7 +93,7 @@
      @@ -210,11 +216,11 @@

      Contents

      -

      Developed by Matt Jones, David Detomaso, Tal Ashuach.

      +

      Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

      -

      Site built with pkgdown 1.5.1.

      +

      Site built with pkgdown 1.6.1.

      diff --git a/docs/reference/sqdist.html b/docs/reference/sqdist.html index 81067c15..2be6384e 100644 --- a/docs/reference/sqdist.html +++ b/docs/reference/sqdist.html @@ -90,7 +90,7 @@
      @@ -190,11 +196,11 @@

      Contents

      -

      Developed by Matt Jones, David Detomaso, Tal Ashuach.

      +

      Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

      -

      Site built with pkgdown 1.5.1.

      +

      Site built with pkgdown 1.6.1.

      diff --git a/docs/reference/translateCellPositions.html b/docs/reference/translateCellPositions.html index 5fe375c9..b3abbb8b 100644 --- a/docs/reference/translateCellPositions.html +++ b/docs/reference/translateCellPositions.html @@ -90,7 +90,7 @@
      @@ -194,11 +200,11 @@

      Contents

      -

      Developed by Matt Jones, David Detomaso, Tal Ashuach.

      +

      Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

      -

      Site built with pkgdown 1.5.1.

      +

      Site built with pkgdown 1.6.1.

      diff --git a/docs/reference/versionCheck.html b/docs/reference/versionCheck.html index 5a2f0342..93ff3c43 100644 --- a/docs/reference/versionCheck.html +++ b/docs/reference/versionCheck.html @@ -90,7 +90,7 @@
      @@ -183,11 +189,11 @@

      Contents

      -

      Developed by Matt Jones, David Detomaso, Tal Ashuach.

      +

      Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

      -

      Site built with pkgdown 1.5.1.

      +

      Site built with pkgdown 1.6.1.

      diff --git a/docs/reference/viewResults.html b/docs/reference/viewResults.html index 26e5ce1a..859bdaa6 100644 --- a/docs/reference/viewResults.html +++ b/docs/reference/viewResults.html @@ -90,7 +90,7 @@
      • - +
        • @@ -116,6 +116,12 @@
      • Incorporating a Trajectory Model
        • +
      • + PhyloVision and Hotspot +
        • +
      • + Spatial Data and Hotspot +
      • How To: Working with Seurat
        • @@ -134,7 +140,7 @@
        • - +
          • @@ -161,10 +167,10 @@

          View results of analysis

          # S4 method for Vision
-viewResults(object, port = NULL, host = NULL, browser = TRUE, name = NULL)
+viewResults(object, port = NULL, host = NULL, browser = TRUE, name = NULL)
 
 # S4 method for character
-viewResults(object, port = NULL, host = NULL, browser = TRUE, name = NULL)
          +viewResults(object, port = NULL, host = NULL, browser = TRUE, name = NULL)

          Arguments

      @@ -199,17 +205,18 @@

      Value

      None

      Examples

      - 
      if (FALSE) {
+    
      if (FALSE) {
 
-vis <- Vision(data = expMat, signatures = sigs)
+vis <- Vision(data = expMat, signatures = sigs)
 
-options(mc.cores=10) # Use 10 cores
-vis <- analyze(vis)
+options(mc.cores=10) # Use 10 cores
+vis <- analyze(vis)
 
-saveRDS(vis, 'vision_results.rds') # (Optional) Save results
+saveRDS(vis, 'vision_results.rds') # (Optional) Save results
 
-vis <- viewResults(vis) # Launches dynamic output report
-}
      
+vis <- viewResults(vis) # Launches dynamic output report
+}
+
      diff --git a/docs/articles/Signatures.html b/docs/articles/Signatures.html index dcf3dc8f..e3bc63d6 100644 --- a/docs/articles/Signatures.html +++ b/docs/articles/Signatures.html @@ -39,7 +39,7 @@ VISION - 2.1.0 + 3.0.0 diff --git a/docs/articles/VISION-vignette.html b/docs/articles/VISION-vignette.html index 05701333..e9f01700 100644 --- a/docs/articles/VISION-vignette.html +++ b/docs/articles/VISION-vignette.html @@ -39,7 +39,7 @@ VISION - 2.1.0 + 3.0.0 diff --git a/docs/articles/index.html b/docs/articles/index.html index ac358c20..8d5afc3a 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -81,7 +81,7 @@ VISION - 2.1.0 + 3.0.0 @@ -170,9 +170,9 @@

      All vignettes

      Micropooling
      -
      VisCas Vignette
      +
      Introduction to PhyloVision and Hotspot
      -
      Vision Hotspot Vignette
      +
      Spatial Data and Hotspot
      Incorporating a Trajectory Model
      diff --git a/docs/articles/micropooling.html b/docs/articles/micropooling.html index de283f9c..67026c9d 100644 --- a/docs/articles/micropooling.html +++ b/docs/articles/micropooling.html @@ -39,7 +39,7 @@ VISION - 2.1.0 + 3.0.0 diff --git a/docs/articles/trajectories.html b/docs/articles/trajectories.html index 875204a5..2a3a6fe0 100644 --- a/docs/articles/trajectories.html +++ b/docs/articles/trajectories.html @@ -39,7 +39,7 @@ VISION - 2.1.0 + 3.0.0 diff --git a/docs/articles/web_only/10xData.html b/docs/articles/web_only/10xData.html index 22525be5..f090eaac 100644 --- a/docs/articles/web_only/10xData.html +++ b/docs/articles/web_only/10xData.html @@ -39,7 +39,7 @@ VISION - 2.1.0 + 3.0.0 diff --git a/docs/articles/web_only/Seurat.html b/docs/articles/web_only/Seurat.html index b15221d7..8e4b0a9c 100644 --- a/docs/articles/web_only/Seurat.html +++ b/docs/articles/web_only/Seurat.html @@ -39,7 +39,7 @@ VISION - 2.1.0 + 3.0.0 diff --git a/docs/articles/web_only/SignatureAutocorrelation.html b/docs/articles/web_only/SignatureAutocorrelation.html index 4d66a492..d1f3accf 100644 --- a/docs/articles/web_only/SignatureAutocorrelation.html +++ b/docs/articles/web_only/SignatureAutocorrelation.html @@ -39,7 +39,7 @@ VISION - 2.1.0 + 3.0.0 diff --git a/docs/authors.html b/docs/authors.html index ffbb3185..d7b4978e 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -81,7 +81,7 @@ VISION - 2.1.0 + 3.0.0 diff --git a/docs/index.html b/docs/index.html index 34298604..2876beae 100644 --- a/docs/index.html +++ b/docs/index.html @@ -39,7 +39,7 @@ VISION - 2.1.0 + 3.0.0 diff --git a/docs/news/index.html b/docs/news/index.html index d8c6c503..8183e9d8 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -81,7 +81,7 @@ VISION - 2.1.0 + 3.0.0 @@ -160,6 +160,13 @@

      Changelog

      Source: NEWS.md +
      +

      +VISION 3.0

      +

      Added support for Phylogenies as latent spaces in core VISION.

      +

      Integrated Hotspot into VISION analysis and report UI.

      +

      Deprecated support for trajectories and LC Annotator.

      +

      VISION 2.1.0

      diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 7b324ed9..176782f3 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -5,13 +5,13 @@ articles: Signatures: Signatures.html VISION-vignette: VISION-vignette.html micropooling: micropooling.html - phlyoVision: phlyoVision.html + phyloVision: phyloVision.html spatialHotspot: spatialHotspot.html trajectories: trajectories.html web_only/10xData: 10xData.html web_only/Seurat: Seurat.html web_only/SignatureAutocorrelation: SignatureAutocorrelation.html -last_built: 2021-06-10T06:27Z +last_built: 2021-06-10T07:06Z urls: reference: https://yoseflab.github.io/VISION//reference article: https://yoseflab.github.io/VISION//articles diff --git a/docs/reference/Cluster.html b/docs/reference/Cluster.html index df84b2a9..6dc6a1be 100644 --- a/docs/reference/Cluster.html +++ b/docs/reference/Cluster.html @@ -85,7 +85,7 @@ VISION - 2.1.0 + 3.0.0
      diff --git a/docs/reference/NormData.html b/docs/reference/NormData.html index fba316f1..b58dde29 100644 --- a/docs/reference/NormData.html +++ b/docs/reference/NormData.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 diff --git a/docs/reference/ServerExpression.html b/docs/reference/ServerExpression.html index 43aa04ef..2ab4ea66 100644 --- a/docs/reference/ServerExpression.html +++ b/docs/reference/ServerExpression.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 diff --git a/docs/reference/ServerSigProjMatrix.html b/docs/reference/ServerSigProjMatrix.html index 4738ed14..30333091 100644 --- a/docs/reference/ServerSigProjMatrix.html +++ b/docs/reference/ServerSigProjMatrix.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 diff --git a/docs/reference/Signature.html b/docs/reference/Signature.html index a4d408fe..7d51ea83 100644 --- a/docs/reference/Signature.html +++ b/docs/reference/Signature.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 diff --git a/docs/reference/Trajectory.html b/docs/reference/Trajectory.html index 430f3ae3..c197375b 100644 --- a/docs/reference/Trajectory.html +++ b/docs/reference/Trajectory.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 diff --git a/docs/reference/TrajectoryProjection.html b/docs/reference/TrajectoryProjection.html index 4f2f5b34..09bc6e27 100644 --- a/docs/reference/TrajectoryProjection.html +++ b/docs/reference/TrajectoryProjection.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 diff --git a/docs/reference/VISION-class.html b/docs/reference/VISION-class.html index f0792284..1a8369e6 100644 --- a/docs/reference/VISION-class.html +++ b/docs/reference/VISION-class.html @@ -85,7 +85,7 @@ VISION - 2.1.0 + 3.0.0 @@ -198,6 +198,7 @@

      Initializes a new VISION object.

      latentTrajectory = NULL, tree = NULL, modData = list(), + hotspot = NULL, pools = list() ) @@ -344,6 +345,10 @@

      Arg

      + + + + - +
      modData

      a list of signature objects for user defined modules
      hotspot

      a list containing one hotspot object precomputed in python and loaded in via reticulate

      pools

      assignments of cell to micropool. Used when microclustering batches diff --git a/docs/reference/VISION.html b/docs/reference/VISION.html index 4fcdec5d..18c16d1a 100644 --- a/docs/reference/VISION.html +++ b/docs/reference/VISION.html @@ -88,7 +88,7 @@ VISION - 2.1.0 + 3.0.0 diff --git a/docs/reference/addLatentSpace.html b/docs/reference/addLatentSpace.html index 5f689547..0d07ee4e 100644 --- a/docs/reference/addLatentSpace.html +++ b/docs/reference/addLatentSpace.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 diff --git a/docs/reference/addProjection-Vision-method.html b/docs/reference/addProjection-Vision-method.html index 81d235f6..c68048b0 100644 --- a/docs/reference/addProjection-Vision-method.html +++ b/docs/reference/addProjection-Vision-method.html @@ -87,7 +87,7 @@ VISION - 2.1.0 + 3.0.0 diff --git a/docs/reference/addSignatures.html b/docs/reference/addSignatures.html index 0c66dd5e..d3043f3d 100644 --- a/docs/reference/addSignatures.html +++ b/docs/reference/addSignatures.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 diff --git a/docs/reference/addTSNE.html b/docs/reference/addTSNE.html index 43439071..57e89357 100644 --- a/docs/reference/addTSNE.html +++ b/docs/reference/addTSNE.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 diff --git a/docs/reference/addUMAP.html b/docs/reference/addUMAP.html index 3dfb7f28..5c852d96 100644 --- a/docs/reference/addUMAP.html +++ b/docs/reference/addUMAP.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 diff --git a/docs/reference/analyze-Vision-method.html b/docs/reference/analyze-Vision-method.html index 6ceb4c18..f9bff987 100644 --- a/docs/reference/analyze-Vision-method.html +++ b/docs/reference/analyze-Vision-method.html @@ -83,7 +83,7 @@ VISION - 2.1.0 + 3.0.0 @@ -180,7 +180,7 @@

      Arg

      tree

      wether to use the TREE slot of the object to calculate values

      whether to use the TREE slot of the object to calculate values
      diff --git a/docs/reference/analyzeLocalCorrelations.html b/docs/reference/analyzeLocalCorrelations.html index 7c43381e..7caf3891 100644 --- a/docs/reference/analyzeLocalCorrelations.html +++ b/docs/reference/analyzeLocalCorrelations.html @@ -85,7 +85,7 @@ VISION - 2.1.0 + 3.0.0 diff --git a/docs/reference/analyzeTrajectoryCorrelations.html b/docs/reference/analyzeTrajectoryCorrelations.html index fb93ae78..01750d27 100644 --- a/docs/reference/analyzeTrajectoryCorrelations.html +++ b/docs/reference/analyzeTrajectoryCorrelations.html @@ -85,7 +85,7 @@ VISION - 2.1.0 + 3.0.0 diff --git a/docs/reference/annotateLatentComponents.html b/docs/reference/annotateLatentComponents.html index 0f9a8601..a85740a5 100644 --- a/docs/reference/annotateLatentComponents.html +++ b/docs/reference/annotateLatentComponents.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 diff --git a/docs/reference/applyFilters.html b/docs/reference/applyFilters.html index ee5f35a2..bdc8c392 100644 --- a/docs/reference/applyFilters.html +++ b/docs/reference/applyFilters.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 diff --git a/docs/reference/applyICA.html b/docs/reference/applyICA.html index 994556b4..caeceb23 100644 --- a/docs/reference/applyICA.html +++ b/docs/reference/applyICA.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 diff --git a/docs/reference/applyISOMap.html b/docs/reference/applyISOMap.html index fdf3afd4..23853220 100644 --- a/docs/reference/applyISOMap.html +++ b/docs/reference/applyISOMap.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 diff --git a/docs/reference/applyMicroClustering.html b/docs/reference/applyMicroClustering.html index c6f579eb..f3ec3806 100644 --- a/docs/reference/applyMicroClustering.html +++ b/docs/reference/applyMicroClustering.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 diff --git a/docs/reference/applyPCA.html b/docs/reference/applyPCA.html index 3ccdb301..2d342ad8 100644 --- a/docs/reference/applyPCA.html +++ b/docs/reference/applyPCA.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 diff --git a/docs/reference/applyPermutationWPCA.html b/docs/reference/applyPermutationWPCA.html index a73b3e12..091a97a9 100644 --- a/docs/reference/applyPermutationWPCA.html +++ b/docs/reference/applyPermutationWPCA.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 diff --git a/docs/reference/applyRBFPCA.html b/docs/reference/applyRBFPCA.html index 863d89b7..16fd9ae5 100644 --- a/docs/reference/applyRBFPCA.html +++ b/docs/reference/applyRBFPCA.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 diff --git a/docs/reference/applySimplePPT.html b/docs/reference/applySimplePPT.html index f9650f19..9149ede4 100644 --- a/docs/reference/applySimplePPT.html +++ b/docs/reference/applySimplePPT.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 diff --git a/docs/reference/applySpectralEmbedding.html b/docs/reference/applySpectralEmbedding.html index 33be6ced..b3896820 100644 --- a/docs/reference/applySpectralEmbedding.html +++ b/docs/reference/applySpectralEmbedding.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 diff --git a/docs/reference/applyUMAP.html b/docs/reference/applyUMAP.html index 37e4c8d3..121d6f00 100644 --- a/docs/reference/applyUMAP.html +++ b/docs/reference/applyUMAP.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 diff --git a/docs/reference/applytSNE10.html b/docs/reference/applytSNE10.html index b4c7d0fe..d0ae0f8a 100644 --- a/docs/reference/applytSNE10.html +++ b/docs/reference/applytSNE10.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 diff --git a/docs/reference/applytSNE30.html b/docs/reference/applytSNE30.html index 9ca37184..aa14d7f8 100644 --- a/docs/reference/applytSNE30.html +++ b/docs/reference/applytSNE30.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 diff --git a/docs/reference/batchSigEvalNorm.html b/docs/reference/batchSigEvalNorm.html index 2ac753f1..773a37fd 100644 --- a/docs/reference/batchSigEvalNorm.html +++ b/docs/reference/batchSigEvalNorm.html @@ -83,7 +83,7 @@ VISION - 2.1.0 + 3.0.0 diff --git a/docs/reference/batchify.html b/docs/reference/batchify.html index d44f8941..56fe6136 100644 --- a/docs/reference/batchify.html +++ b/docs/reference/batchify.html @@ -84,7 +84,7 @@ VISION - 2.1.0 + 3.0.0 diff --git a/docs/reference/calcInterEdgeDistMat.html b/docs/reference/calcInterEdgeDistMat.html index 8d5722f6..c511c4b8 100644 --- a/docs/reference/calcInterEdgeDistMat.html +++ b/docs/reference/calcInterEdgeDistMat.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 diff --git a/docs/reference/calcIntraEdgeDistMat.html b/docs/reference/calcIntraEdgeDistMat.html index 862ff3b3..43f52d49 100644 --- a/docs/reference/calcIntraEdgeDistMat.html +++ b/docs/reference/calcIntraEdgeDistMat.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 diff --git a/docs/reference/calcSignatureScores.html b/docs/reference/calcSignatureScores.html index aacbd16b..803c779c 100644 --- a/docs/reference/calcSignatureScores.html +++ b/docs/reference/calcSignatureScores.html @@ -83,7 +83,7 @@ VISION - 2.1.0 + 3.0.0 diff --git a/docs/reference/calculateTrajectoryDistances.html b/docs/reference/calculateTrajectoryDistances.html index 60a74bc5..f62f7bfe 100644 --- a/docs/reference/calculateTrajectoryDistances.html +++ b/docs/reference/calculateTrajectoryDistances.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 diff --git a/docs/reference/clipBottom.html b/docs/reference/clipBottom.html index edaf30bf..c311c23e 100644 --- a/docs/reference/clipBottom.html +++ b/docs/reference/clipBottom.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 diff --git a/docs/reference/clusterCells.html b/docs/reference/clusterCells.html index 1e51f6db..0961837f 100644 --- a/docs/reference/clusterCells.html +++ b/docs/reference/clusterCells.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 diff --git a/docs/reference/clusterSigScores.html b/docs/reference/clusterSigScores.html index 046e1a8e..fb852aaa 100644 --- a/docs/reference/clusterSigScores.html +++ b/docs/reference/clusterSigScores.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 diff --git a/docs/reference/clusterSignatures.html b/docs/reference/clusterSignatures.html index 19119582..45983b91 100644 --- a/docs/reference/clusterSignatures.html +++ b/docs/reference/clusterSignatures.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 diff --git a/docs/reference/colNormalization.html b/docs/reference/colNormalization.html index 713c35ed..ad23cdf3 100644 --- a/docs/reference/colNormalization.html +++ b/docs/reference/colNormalization.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 diff --git a/docs/reference/colRankNormalization.html b/docs/reference/colRankNormalization.html index a2f0a6e4..4d2004f5 100644 --- a/docs/reference/colRankNormalization.html +++ b/docs/reference/colRankNormalization.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 diff --git a/docs/reference/colVarsSp.html b/docs/reference/colVarsSp.html index bb8af4e1..872f73e2 100644 --- a/docs/reference/colVarsSp.html +++ b/docs/reference/colVarsSp.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 diff --git a/docs/reference/computeKNNWeights-Trajectory-method.html b/docs/reference/computeKNNWeights-Trajectory-method.html index 7b7a3ba0..3076c98c 100644 --- a/docs/reference/computeKNNWeights-Trajectory-method.html +++ b/docs/reference/computeKNNWeights-Trajectory-method.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 diff --git a/docs/reference/computeKNNWeights-matrix-method.html b/docs/reference/computeKNNWeights-matrix-method.html index e974ea79..f846e62f 100644 --- a/docs/reference/computeKNNWeights-matrix-method.html +++ b/docs/reference/computeKNNWeights-matrix-method.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 diff --git a/docs/reference/computeLatentSpace.html b/docs/reference/computeLatentSpace.html index 8459df10..6cc19eda 100644 --- a/docs/reference/computeLatentSpace.html +++ b/docs/reference/computeLatentSpace.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 diff --git a/docs/reference/computeProjectionGenes.html b/docs/reference/computeProjectionGenes.html index e8b187b2..78f3e751 100644 --- a/docs/reference/computeProjectionGenes.html +++ b/docs/reference/computeProjectionGenes.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 diff --git a/docs/reference/convertGeneIds.html b/docs/reference/convertGeneIds.html index 168a71a5..25b8e60c 100644 --- a/docs/reference/convertGeneIds.html +++ b/docs/reference/convertGeneIds.html @@ -83,7 +83,7 @@ VISION - 2.1.0 + 3.0.0 diff --git a/docs/reference/coordinatesToJSON.html b/docs/reference/coordinatesToJSON.html index 00ffa04f..4622acc0 100644 --- a/docs/reference/coordinatesToJSON.html +++ b/docs/reference/coordinatesToJSON.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 diff --git a/docs/reference/createGeneSignature.html b/docs/reference/createGeneSignature.html index 9a8e106a..d2df6692 100644 --- a/docs/reference/createGeneSignature.html +++ b/docs/reference/createGeneSignature.html @@ -85,7 +85,7 @@ VISION - 2.1.0 + 3.0.0 diff --git a/docs/reference/createTrajectoryMetaData.html b/docs/reference/createTrajectoryMetaData.html index fcde7190..d4c849c7 100644 --- a/docs/reference/createTrajectoryMetaData.html +++ b/docs/reference/createTrajectoryMetaData.html @@ -83,7 +83,7 @@ VISION - 2.1.0 + 3.0.0 diff --git a/docs/reference/dot-colNormHelper.html b/docs/reference/dot-colNormHelper.html index 2220d83c..5d5b6423 100644 --- a/docs/reference/dot-colNormHelper.html +++ b/docs/reference/dot-colNormHelper.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 diff --git a/docs/reference/evalSigGeneImportance.html b/docs/reference/evalSigGeneImportance.html index 9c1ce824..914f1f3a 100644 --- a/docs/reference/evalSigGeneImportance.html +++ b/docs/reference/evalSigGeneImportance.html @@ -84,7 +84,7 @@ VISION - 2.1.0 + 3.0.0 diff --git a/docs/reference/evalSigGeneImportanceSparse.html b/docs/reference/evalSigGeneImportanceSparse.html index 273aa9fc..466f0767 100644 --- a/docs/reference/evalSigGeneImportanceSparse.html +++ b/docs/reference/evalSigGeneImportanceSparse.html @@ -84,7 +84,7 @@ VISION - 2.1.0 + 3.0.0 diff --git a/docs/reference/fbConsistencyScores.html b/docs/reference/fbConsistencyScores.html index 7c55874a..cd99feed 100644 --- a/docs/reference/fbConsistencyScores.html +++ b/docs/reference/fbConsistencyScores.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 diff --git a/docs/reference/filterGenesFano.html b/docs/reference/filterGenesFano.html index a181f47c..abc2cd16 100644 --- a/docs/reference/filterGenesFano.html +++ b/docs/reference/filterGenesFano.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 diff --git a/docs/reference/filterGenesNovar.html b/docs/reference/filterGenesNovar.html index eb84b18d..58910f2f 100644 --- a/docs/reference/filterGenesNovar.html +++ b/docs/reference/filterGenesNovar.html @@ -88,7 +88,7 @@ VISION - 2.1.0 + 3.0.0 diff --git a/docs/reference/filterGenesThreshold.html b/docs/reference/filterGenesThreshold.html index 98167923..cb19270a 100644 --- a/docs/reference/filterGenesThreshold.html +++ b/docs/reference/filterGenesThreshold.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 diff --git a/docs/reference/find_knn_parallel.html b/docs/reference/find_knn_parallel.html index bbadbb38..eb3b2452 100644 --- a/docs/reference/find_knn_parallel.html +++ b/docs/reference/find_knn_parallel.html @@ -84,7 +84,7 @@ VISION - 2.1.0 + 3.0.0 diff --git a/docs/reference/fitTree.html b/docs/reference/fitTree.html index ae22c586..95a63543 100644 --- a/docs/reference/fitTree.html +++ b/docs/reference/fitTree.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 diff --git a/docs/reference/geary_sig_v_proj.html b/docs/reference/geary_sig_v_proj.html index 83280cee..dd74bb23 100644 --- a/docs/reference/geary_sig_v_proj.html +++ b/docs/reference/geary_sig_v_proj.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 diff --git a/docs/reference/generatePermutationNull.html b/docs/reference/generatePermutationNull.html index 07aa63f8..a7112f94 100644 --- a/docs/reference/generatePermutationNull.html +++ b/docs/reference/generatePermutationNull.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 diff --git a/docs/reference/generateProjections.html b/docs/reference/generateProjections.html index 8d168d2d..231091c8 100644 --- a/docs/reference/generateProjections.html +++ b/docs/reference/generateProjections.html @@ -83,7 +83,7 @@ VISION - 2.1.0 + 3.0.0 diff --git a/docs/reference/generateProjectionsInner.html b/docs/reference/generateProjectionsInner.html index 5c8d0575..ce04fdd7 100644 --- a/docs/reference/generateProjectionsInner.html +++ b/docs/reference/generateProjectionsInner.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 diff --git a/docs/reference/generateTrajectoryProjections.html b/docs/reference/generateTrajectoryProjections.html index 7234223f..4e3a004d 100644 --- a/docs/reference/generateTrajectoryProjections.html +++ b/docs/reference/generateTrajectoryProjections.html @@ -83,7 +83,7 @@ VISION - 2.1.0 + 3.0.0 diff --git a/docs/reference/getLatentSpace.html b/docs/reference/getLatentSpace.html index 111765e7..924ee5d2 100644 --- a/docs/reference/getLatentSpace.html +++ b/docs/reference/getLatentSpace.html @@ -83,7 +83,7 @@ VISION - 2.1.0 + 3.0.0 diff --git a/docs/reference/getLatentTrajectory.html b/docs/reference/getLatentTrajectory.html index 37984ecb..9d77f033 100644 --- a/docs/reference/getLatentTrajectory.html +++ b/docs/reference/getLatentTrajectory.html @@ -83,7 +83,7 @@ VISION - 2.1.0 + 3.0.0 diff --git a/docs/reference/getMSE.html b/docs/reference/getMSE.html index 85f1c789..5239a894 100644 --- a/docs/reference/getMSE.html +++ b/docs/reference/getMSE.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 diff --git a/docs/reference/getMetaAutocorrelation.html b/docs/reference/getMetaAutocorrelation.html index 0948cb0f..09e64eb6 100644 --- a/docs/reference/getMetaAutocorrelation.html +++ b/docs/reference/getMetaAutocorrelation.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 diff --git a/docs/reference/getMetaDifferential.html b/docs/reference/getMetaDifferential.html index 44bb2db2..40f53f01 100644 --- a/docs/reference/getMetaDifferential.html +++ b/docs/reference/getMetaDifferential.html @@ -83,7 +83,7 @@ VISION - 2.1.0 + 3.0.0 diff --git a/docs/reference/getNormalizedCopy.html b/docs/reference/getNormalizedCopy.html index b6bf8d96..3a14d18b 100644 --- a/docs/reference/getNormalizedCopy.html +++ b/docs/reference/getNormalizedCopy.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 diff --git a/docs/reference/getNormalizedCopySparse.html b/docs/reference/getNormalizedCopySparse.html index 6f7985fa..a8589bf1 100644 --- a/docs/reference/getNormalizedCopySparse.html +++ b/docs/reference/getNormalizedCopySparse.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 diff --git a/docs/reference/getParam.html b/docs/reference/getParam.html index 633a8509..25963625 100644 --- a/docs/reference/getParam.html +++ b/docs/reference/getParam.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 diff --git a/docs/reference/getProjections.html b/docs/reference/getProjections.html index 5f1ad7af..97d93b8d 100644 --- a/docs/reference/getProjections.html +++ b/docs/reference/getProjections.html @@ -83,7 +83,7 @@ VISION - 2.1.0 + 3.0.0 diff --git a/docs/reference/getSelections.html b/docs/reference/getSelections.html index fd66783c..d42303da 100644 --- a/docs/reference/getSelections.html +++ b/docs/reference/getSelections.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 diff --git a/docs/reference/getSignatureAutocorrelation.html b/docs/reference/getSignatureAutocorrelation.html index a4e6116a..c54b5764 100644 --- a/docs/reference/getSignatureAutocorrelation.html +++ b/docs/reference/getSignatureAutocorrelation.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 diff --git a/docs/reference/getSignatureDifferential.html b/docs/reference/getSignatureDifferential.html index a8987646..94988765 100644 --- a/docs/reference/getSignatureDifferential.html +++ b/docs/reference/getSignatureDifferential.html @@ -83,7 +83,7 @@ VISION - 2.1.0 + 3.0.0 diff --git a/docs/reference/getSignatureScores.html b/docs/reference/getSignatureScores.html index e9fedfa1..609ef0c5 100644 --- a/docs/reference/getSignatureScores.html +++ b/docs/reference/getSignatureScores.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 diff --git a/docs/reference/hasUnnormalizedData.html b/docs/reference/hasUnnormalizedData.html index 5badd48c..bf2a0fe5 100644 --- a/docs/reference/hasUnnormalizedData.html +++ b/docs/reference/hasUnnormalizedData.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 diff --git a/docs/reference/ilog1p.html b/docs/reference/ilog1p.html index 0733f500..6b76ac9c 100644 --- a/docs/reference/ilog1p.html +++ b/docs/reference/ilog1p.html @@ -83,7 +83,7 @@ VISION - 2.1.0 + 3.0.0 diff --git a/docs/reference/index.html b/docs/reference/index.html index 7893cbb1..83b4001d 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -81,7 +81,7 @@ VISION - 2.1.0 + 3.0.0 @@ -339,7 +339,19 @@

+

PhyloVision()

+

Initializes a new PhyloVision Object

+

phyloAnalyze(<PhyloVision>)

+

Analyze a PhyloVision object
@@ -352,7 +364,65 @@

runHotspot()

+ +

Perform Hotspot analysis on Vision Object

+

hsInit()

+

Init Hotspot object from Vision Object

+

hsCreateKnnGraph()

+

Init KNN graph in Hotspot object

+

hsComputeAutoCorrelations()

+

Compute Hotspot auto correlations

+

hsComputeLocalCorrelations()

+

Interface function to compute local correlations for Hotspot +Warning: modifies the hs argument

+

hsCalculateModuleScores()

+

Create Hotspot Modules and calculate module scores given a HS object +with local correlations already calculated

+

analyzeHotspotObjectVision()

+

Analyze a Hotspot object using built in methods such +such as local correlation, signature overlap, etc. +Necessary to run this function for Hotspot functionality in viewer to work.

+

loadHotspotObject()

+

Load in an existing Hotspot object from bytes or a file

+

draw_hotspot_heatmap()

+

Draw Modules Heatmap (Gene x Gene)
diff --git a/docs/reference/innerEvalSignatureBatchNorm.html b/docs/reference/innerEvalSignatureBatchNorm.html index d5f2bde7..0493c2f7 100644 --- a/docs/reference/innerEvalSignatureBatchNorm.html +++ b/docs/reference/innerEvalSignatureBatchNorm.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 diff --git a/docs/reference/launchServer.html b/docs/reference/launchServer.html index 1d5980e2..f3dea4d5 100644 --- a/docs/reference/launchServer.html +++ b/docs/reference/launchServer.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 diff --git a/docs/reference/louvainCluster.html b/docs/reference/louvainCluster.html index a1c8ccdc..c2fbe510 100644 --- a/docs/reference/louvainCluster.html +++ b/docs/reference/louvainCluster.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 diff --git a/docs/reference/matLog2.html b/docs/reference/matLog2.html index 384241f1..e543bd3a 100644 --- a/docs/reference/matLog2.html +++ b/docs/reference/matLog2.html @@ -83,7 +83,7 @@ VISION - 2.1.0 + 3.0.0 diff --git a/docs/reference/matrix_chisq.html b/docs/reference/matrix_chisq.html index c9a1c64b..98c360ee 100644 --- a/docs/reference/matrix_chisq.html +++ b/docs/reference/matrix_chisq.html @@ -83,7 +83,7 @@ VISION - 2.1.0 + 3.0.0 diff --git a/docs/reference/matrix_wilcox.html b/docs/reference/matrix_wilcox.html index 02153d73..4bb4c074 100644 --- a/docs/reference/matrix_wilcox.html +++ b/docs/reference/matrix_wilcox.html @@ -83,7 +83,7 @@ VISION - 2.1.0 + 3.0.0 diff --git a/docs/reference/matrix_wilcox_cpp.html b/docs/reference/matrix_wilcox_cpp.html index 43c94643..788d3291 100644 --- a/docs/reference/matrix_wilcox_cpp.html +++ b/docs/reference/matrix_wilcox_cpp.html @@ -83,7 +83,7 @@ VISION - 2.1.0 + 3.0.0 diff --git a/docs/reference/noNormalization.html b/docs/reference/noNormalization.html index 5190ac71..3d0a38b4 100644 --- a/docs/reference/noNormalization.html +++ b/docs/reference/noNormalization.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 diff --git a/docs/reference/pearsonCorrToJSON.html b/docs/reference/pearsonCorrToJSON.html index a3eb2667..8686d1ba 100644 --- a/docs/reference/pearsonCorrToJSON.html +++ b/docs/reference/pearsonCorrToJSON.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 diff --git a/docs/reference/poolCells.html b/docs/reference/poolCells.html index 1a400e00..802d4ff7 100644 --- a/docs/reference/poolCells.html +++ b/docs/reference/poolCells.html @@ -85,7 +85,7 @@ VISION - 2.1.0 + 3.0.0 diff --git a/docs/reference/poolMatrixCols.html b/docs/reference/poolMatrixCols.html index 43f19245..56212f90 100644 --- a/docs/reference/poolMatrixCols.html +++ b/docs/reference/poolMatrixCols.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 diff --git a/docs/reference/poolMatrixCols_Inner.html b/docs/reference/poolMatrixCols_Inner.html index a87c4e67..3d9376a4 100644 --- a/docs/reference/poolMatrixCols_Inner.html +++ b/docs/reference/poolMatrixCols_Inner.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 diff --git a/docs/reference/poolMatrixRows.html b/docs/reference/poolMatrixRows.html index 2df19d0a..4ef56a0f 100644 --- a/docs/reference/poolMatrixRows.html +++ b/docs/reference/poolMatrixRows.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 diff --git a/docs/reference/poolMetaData.html b/docs/reference/poolMetaData.html index f9aeef5e..ebd89605 100644 --- a/docs/reference/poolMetaData.html +++ b/docs/reference/poolMetaData.html @@ -83,7 +83,7 @@ VISION - 2.1.0 + 3.0.0 diff --git a/docs/reference/processSignatures.html b/docs/reference/processSignatures.html index bbd0c79d..3ac716ea 100644 --- a/docs/reference/processSignatures.html +++ b/docs/reference/processSignatures.html @@ -83,7 +83,7 @@ VISION - 2.1.0 + 3.0.0 diff --git a/docs/reference/projectOnTree.html b/docs/reference/projectOnTree.html index 11ba8fcc..fdccb8ea 100644 --- a/docs/reference/projectOnTree.html +++ b/docs/reference/projectOnTree.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 diff --git a/docs/reference/readSignaturesInput.html b/docs/reference/readSignaturesInput.html index f00cc344..d0389658 100644 --- a/docs/reference/readSignaturesInput.html +++ b/docs/reference/readSignaturesInput.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 diff --git a/docs/reference/read_10x.html b/docs/reference/read_10x.html index 6c566c9c..8abc359b 100644 --- a/docs/reference/read_10x.html +++ b/docs/reference/read_10x.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 diff --git a/docs/reference/read_10x_h5.html b/docs/reference/read_10x_h5.html index 071046a3..d1c38754 100644 --- a/docs/reference/read_10x_h5.html +++ b/docs/reference/read_10x_h5.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 diff --git a/docs/reference/read_10x_h5_v2.html b/docs/reference/read_10x_h5_v2.html index 3ae0377e..ab294a63 100644 --- a/docs/reference/read_10x_h5_v2.html +++ b/docs/reference/read_10x_h5_v2.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 diff --git a/docs/reference/read_10x_h5_v3.html b/docs/reference/read_10x_h5_v3.html index 135adac9..0f2b5081 100644 --- a/docs/reference/read_10x_h5_v3.html +++ b/docs/reference/read_10x_h5_v3.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 diff --git a/docs/reference/readjust_clusters.html b/docs/reference/readjust_clusters.html index 3b316ec4..1cdeb1a6 100644 --- a/docs/reference/readjust_clusters.html +++ b/docs/reference/readjust_clusters.html @@ -83,7 +83,7 @@ VISION - 2.1.0 + 3.0.0 diff --git a/docs/reference/registerMethods.html b/docs/reference/registerMethods.html index 2d30cca7..7048b2d2 100644 --- a/docs/reference/registerMethods.html +++ b/docs/reference/registerMethods.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 diff --git a/docs/reference/rowAndColNormalization.html b/docs/reference/rowAndColNormalization.html index 7246ed7a..b2d5531d 100644 --- a/docs/reference/rowAndColNormalization.html +++ b/docs/reference/rowAndColNormalization.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 diff --git a/docs/reference/rowNormalization.html b/docs/reference/rowNormalization.html index 8b0137a2..a1e50c06 100644 --- a/docs/reference/rowNormalization.html +++ b/docs/reference/rowNormalization.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 diff --git a/docs/reference/rowVarsSp.html b/docs/reference/rowVarsSp.html index 3ab03830..79cd9536 100644 --- a/docs/reference/rowVarsSp.html +++ b/docs/reference/rowVarsSp.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 diff --git a/docs/reference/saveAndViewResults-Vision-method.html b/docs/reference/saveAndViewResults-Vision-method.html index 71a7aa49..ce9ef87c 100644 --- a/docs/reference/saveAndViewResults-Vision-method.html +++ b/docs/reference/saveAndViewResults-Vision-method.html @@ -84,7 +84,7 @@ VISION - 2.1.0 + 3.0.0 diff --git a/docs/reference/sigConsistencyScores.html b/docs/reference/sigConsistencyScores.html index 34e26a34..50b4c5e7 100644 --- a/docs/reference/sigConsistencyScores.html +++ b/docs/reference/sigConsistencyScores.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 diff --git a/docs/reference/sigProjMatrixToJSON.html b/docs/reference/sigProjMatrixToJSON.html index 4a440880..cea290b7 100644 --- a/docs/reference/sigProjMatrixToJSON.html +++ b/docs/reference/sigProjMatrixToJSON.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 diff --git a/docs/reference/sigScoresToJSON.html b/docs/reference/sigScoresToJSON.html index 51c719a8..eabb12b6 100644 --- a/docs/reference/sigScoresToJSON.html +++ b/docs/reference/sigScoresToJSON.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 diff --git a/docs/reference/signatureToJSON.html b/docs/reference/signatureToJSON.html index 0ab81c9b..f2464339 100644 --- a/docs/reference/signatureToJSON.html +++ b/docs/reference/signatureToJSON.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 diff --git a/docs/reference/sigsToSparseMatrix.html b/docs/reference/sigsToSparseMatrix.html index aa880546..8cb220b8 100644 --- a/docs/reference/sigsToSparseMatrix.html +++ b/docs/reference/sigsToSparseMatrix.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 diff --git a/docs/reference/sigsVsProjection_n.html b/docs/reference/sigsVsProjection_n.html index 463f6d65..df2480da 100644 --- a/docs/reference/sigsVsProjection_n.html +++ b/docs/reference/sigsVsProjection_n.html @@ -85,7 +85,7 @@ VISION - 2.1.0 + 3.0.0 diff --git a/docs/reference/sigsVsProjection_pcf.html b/docs/reference/sigsVsProjection_pcf.html index 6025e730..be19a322 100644 --- a/docs/reference/sigsVsProjection_pcf.html +++ b/docs/reference/sigsVsProjection_pcf.html @@ -85,7 +85,7 @@ VISION - 2.1.0 + 3.0.0 diff --git a/docs/reference/sigsVsProjection_pcn.html b/docs/reference/sigsVsProjection_pcn.html index f29093a1..18419cd2 100644 --- a/docs/reference/sigsVsProjection_pcn.html +++ b/docs/reference/sigsVsProjection_pcn.html @@ -85,7 +85,7 @@ VISION - 2.1.0 + 3.0.0 diff --git a/docs/reference/sqdist.html b/docs/reference/sqdist.html index 2be6384e..58032bb4 100644 --- a/docs/reference/sqdist.html +++ b/docs/reference/sqdist.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 diff --git a/docs/reference/translateCellPositions.html b/docs/reference/translateCellPositions.html index b3abbb8b..541fa113 100644 --- a/docs/reference/translateCellPositions.html +++ b/docs/reference/translateCellPositions.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 diff --git a/docs/reference/versionCheck.html b/docs/reference/versionCheck.html index 93ff3c43..88e61294 100644 --- a/docs/reference/versionCheck.html +++ b/docs/reference/versionCheck.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 diff --git a/docs/reference/viewResults.html b/docs/reference/viewResults.html index 859bdaa6..b0efee08 100644 --- a/docs/reference/viewResults.html +++ b/docs/reference/viewResults.html @@ -82,7 +82,7 @@ VISION - 2.1.0 + 3.0.0 diff --git a/docs/sitemap.xml b/docs/sitemap.xml index 923b5094..e5bb7ba8 100644 --- a/docs/sitemap.xml +++ b/docs/sitemap.xml @@ -9,6 +9,9 @@ https://yoseflab.github.io/VISION//reference/NormData.html + + https://yoseflab.github.io/VISION//reference/PhyloVision-class.html + https://yoseflab.github.io/VISION//reference/ServerExpression.html @@ -30,6 +33,9 @@ https://yoseflab.github.io/VISION//reference/VISION.html + + https://yoseflab.github.io/VISION//reference/addHotspotToVision.html + https://yoseflab.github.io/VISION//reference/addLatentSpace.html @@ -48,12 +54,21 @@ https://yoseflab.github.io/VISION//reference/analyze-Vision-method.html + + https://yoseflab.github.io/VISION//reference/analyzeHotspotObjectVision.html + https://yoseflab.github.io/VISION//reference/analyzeLocalCorrelations.html + + https://yoseflab.github.io/VISION//reference/analyzeLocalCorrelationsModules.html + https://yoseflab.github.io/VISION//reference/analyzeTrajectoryCorrelations.html + + https://yoseflab.github.io/VISION//reference/ancestor_at_depth.html + https://yoseflab.github.io/VISION//reference/annotateLatentComponents.html @@ -105,9 +120,18 @@ https://yoseflab.github.io/VISION//reference/calcIntraEdgeDistMat.html + + https://yoseflab.github.io/VISION//reference/calcModuleScores.html + https://yoseflab.github.io/VISION//reference/calcSignatureScores.html + + https://yoseflab.github.io/VISION//reference/calc_mod_sig_enrichment.html + + + https://yoseflab.github.io/VISION//reference/calc_set_enrichment.html + https://yoseflab.github.io/VISION//reference/calculateTrajectoryDistances.html @@ -117,6 +141,9 @@ https://yoseflab.github.io/VISION//reference/clusterCells.html + + https://yoseflab.github.io/VISION//reference/clusterModScores.html + https://yoseflab.github.io/VISION//reference/clusterSigScores.html @@ -138,6 +165,9 @@ https://yoseflab.github.io/VISION//reference/computeKNNWeights-matrix-method.html + + https://yoseflab.github.io/VISION//reference/computeKNNWeights-phylo-method.html + https://yoseflab.github.io/VISION//reference/computeLatentSpace.html @@ -156,9 +186,18 @@ https://yoseflab.github.io/VISION//reference/createTrajectoryMetaData.html + + https://yoseflab.github.io/VISION//reference/depthBasedCladewiseTreeCluster.html + + + https://yoseflab.github.io/VISION//reference/depthBasedTreeCluster.html + https://yoseflab.github.io/VISION//reference/dot-colNormHelper.html + + https://yoseflab.github.io/VISION//reference/draw_hotspot_heatmap.html + https://yoseflab.github.io/VISION//reference/evalSigGeneImportance.html @@ -180,12 +219,21 @@ https://yoseflab.github.io/VISION//reference/find_knn_parallel.html + + https://yoseflab.github.io/VISION//reference/find_knn_parallel_tree.html + + + https://yoseflab.github.io/VISION//reference/find_root.html + https://yoseflab.github.io/VISION//reference/fitTree.html https://yoseflab.github.io/VISION//reference/geary_sig_v_proj.html + + https://yoseflab.github.io/VISION//reference/generateOverlapSignatures.html + https://yoseflab.github.io/VISION//reference/generatePermutationNull.html @@ -237,18 +285,69 @@ https://yoseflab.github.io/VISION//reference/getSignatureScores.html + + https://yoseflab.github.io/VISION//reference/get_all_children.html + + + https://yoseflab.github.io/VISION//reference/get_children.html + + + https://yoseflab.github.io/VISION//reference/get_max_cluster_size.html + + + https://yoseflab.github.io/VISION//reference/get_min_cluster_size.html + + + https://yoseflab.github.io/VISION//reference/get_parent.html + + + https://yoseflab.github.io/VISION//reference/group_modules_enrichment.html + https://yoseflab.github.io/VISION//reference/hasUnnormalizedData.html + + https://yoseflab.github.io/VISION//reference/hsCalculateModuleScores.html + + + https://yoseflab.github.io/VISION//reference/hsComputeAutoCorrelations.html + + + https://yoseflab.github.io/VISION//reference/hsComputeLocalCorrelations.html + + + https://yoseflab.github.io/VISION//reference/hsCreateKnnGraph.html + + + https://yoseflab.github.io/VISION//reference/hsInit.html + https://yoseflab.github.io/VISION//reference/ilog1p.html https://yoseflab.github.io/VISION//reference/innerEvalSignatureBatchNorm.html + + https://yoseflab.github.io/VISION//reference/is_tip.html + + + https://yoseflab.github.io/VISION//reference/knn_tree.html + https://yoseflab.github.io/VISION//reference/launchServer.html + + https://yoseflab.github.io/VISION//reference/lcaBasedHotspotNeighbors.html + + + https://yoseflab.github.io/VISION//reference/lcaBasedTreeKNN.html + + + https://yoseflab.github.io/VISION//reference/lca_based_depth.html + + + https://yoseflab.github.io/VISION//reference/loadHotspotObject.html + https://yoseflab.github.io/VISION//reference/louvainCluster.html @@ -264,12 +363,21 @@ https://yoseflab.github.io/VISION//reference/matrix_wilcox_cpp.html + + https://yoseflab.github.io/VISION//reference/maxSizeCladewiseTreeCluster.html + + + https://yoseflab.github.io/VISION//reference/minSizeCladeNeighbors.html + https://yoseflab.github.io/VISION//reference/noNormalization.html https://yoseflab.github.io/VISION//reference/pearsonCorrToJSON.html + + https://yoseflab.github.io/VISION//reference/phyloAnalyze-PhyloVision-method.html + https://yoseflab.github.io/VISION//reference/poolCells.html @@ -321,9 +429,15 @@ https://yoseflab.github.io/VISION//reference/rowVarsSp.html + + https://yoseflab.github.io/VISION//reference/runHotspot.html + https://yoseflab.github.io/VISION//reference/saveAndViewResults-Vision-method.html + + https://yoseflab.github.io/VISION//reference/saveHSBytestToPickle.html + https://yoseflab.github.io/VISION//reference/sigConsistencyScores.html @@ -354,6 +468,15 @@ https://yoseflab.github.io/VISION//reference/translateCellPositions.html + + https://yoseflab.github.io/VISION//reference/treeClusterMinCladeSize.html + + + https://yoseflab.github.io/VISION//reference/trivial_dist.html + + + https://yoseflab.github.io/VISION//reference/ultrametric_tree.html + https://yoseflab.github.io/VISION//reference/versionCheck.html @@ -370,7 +493,7 @@ https://yoseflab.github.io/VISION//articles/micropooling.html - https://yoseflab.github.io/VISION//articles/phlyoVision.html + https://yoseflab.github.io/VISION//articles/phyloVision.html https://yoseflab.github.io/VISION//articles/spatialHotspot.html diff --git a/man/VISION-class.Rd b/man/VISION-class.Rd index 8ade1d67..098cbf55 100644 --- a/man/VISION-class.Rd +++ b/man/VISION-class.Rd @@ -37,6 +37,7 @@ Vision(data, ...) latentTrajectory = NULL, tree = NULL, modData = list(), + hotspot = NULL, pools = list() ) @@ -132,6 +133,8 @@ of a trajectory inference method by the dynverse/dynwrap library} \item{modData}{a list of signature objects for user defined modules} +\item{hotspot}{a list containing one hotspot object precomputed in python and loaded in via reticulate} + \item{pools}{assignments of cell to micropool. Used when microclustering batches separately and then combining. See vignette for usage.} diff --git a/man/analyze-Vision-method.Rd b/man/analyze-Vision-method.Rd index 0e441e78..49c0cf5d 100644 --- a/man/analyze-Vision-method.Rd +++ b/man/analyze-Vision-method.Rd @@ -10,7 +10,7 @@ \arguments{ \item{object}{VISION object} -\item{tree}{wether to use the TREE slot of the object to calculate values} +\item{tree}{whether to use the TREE slot of the object to calculate values} } \value{ VISION object diff --git a/pkgdown/_pkgdown.yml b/pkgdown/_pkgdown.yml index 5007cca9..05aee332 100644 --- a/pkgdown/_pkgdown.yml +++ b/pkgdown/_pkgdown.yml @@ -37,7 +37,6 @@ reference: - title: Hotspot contents: - runHotspot - - phyloAnalyze - hsInit - hsCreateKnnGraph - hsComputeAutoCorrelations diff --git a/vignettes/phyloVision.Rmd b/vignettes/phyloVision.Rmd index e7e92dfd..7432613d 100644 --- a/vignettes/phyloVision.Rmd +++ b/vignettes/phyloVision.Rmd @@ -1,8 +1,11 @@ --- -title: "VisCas Vignette" -author: "Yanay Rosen" -date: "9/30/2020" -output: html_document +title: "Introduction to PhyloVision and Hotspot" +package: "`r BiocStyle::pkg_ver('BiocStyle')`" +output: BiocStyle::html_document +vignette: > + %\VignetteIndexEntry{Introduction to PhyloVision and Hotspot} + %\VignetteEngine{knitr::rmarkdown} + %\VignetteEncoding{UTF-8} --- ```{r setup, include=FALSE} @@ -12,9 +15,9 @@ library(ape) library(reticulate) ``` -## Creating a Phylo Vision Object with a Tree +## Creating a PhyloVision Object with a Tree -Vision objects now support dendrograms for visualization and analysis. To create the Phylo-VISION object, you need all of the same data, an expression matrix, and metadata and/or signatures, but you also include a tree object from the Ape package. +Vision objects now support dendrograms for visualization and analysis. To create the PhyloVision object, you need all of the same data, an expression matrix, and metadata and/or signatures, but you also include a tree object from the Ape package. ```{r create, eval=F} # Read the expression and meta data file_path <- "data/embryogenesis" # Replace the path diff --git a/vignettes/spatialHotspot.Rmd b/vignettes/spatialHotspot.Rmd index 2e9aa45f..7e8c3ef3 100644 --- a/vignettes/spatialHotspot.Rmd +++ b/vignettes/spatialHotspot.Rmd @@ -1,10 +1,14 @@ --- -title: "Vision Hotspot Vignette" -author: "Yanay Rosen" -date: "9/30/2020" -output: html_document +title: "Spatial Data and Hotspot" +package: "`r BiocStyle::pkg_ver('BiocStyle')`" +output: BiocStyle::html_document +vignette: > + %\VignetteIndexEntry{Spatial Data and Hotspot} + %\VignetteEngine{knitr::rmarkdown} + %\VignetteEncoding{UTF-8} --- + ```{r setup, include=FALSE} knitr::opts_chunk$set(echo = TRUE) library(VISION) From 415283c167d52bbb03d024197e060cac8ef05cc3 Mon Sep 17 00:00:00 2001 From: Yanay1 Date: Fri, 11 Jun 2021 11:04:49 -0700 Subject: [PATCH 45/62] updating docs --- NEWS.md | 2 +- R/methods-Module.R | 6 ++++-- vignettes/phyloVision.Rmd | 4 ++-- 3 files changed, 7 insertions(+), 5 deletions(-) diff --git a/NEWS.md b/NEWS.md index 231c28d1..6cfb87c6 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# VISION 3.0 +# VISION 3.0.0 Added support for Phylogenies as latent spaces in core VISION. diff --git a/R/methods-Module.R b/R/methods-Module.R index 1a8d14ef..e870adb1 100644 --- a/R/methods-Module.R +++ b/R/methods-Module.R @@ -736,6 +736,7 @@ draw_hotspot_heatmap <- function(hs, palette = paletteer_d("ggsci::default_nejm" gene_order = colnames(lcz)[np$array(py_dend$leaves)+1] col_mapping = c() module_to_col = list() + hs$modules = as.character(hs$modules) unique_mods = as.character(unique(hs$modules)) example_genes = list() col_mapping[["-1"]] = "#ffffff" @@ -749,9 +750,10 @@ draw_hotspot_heatmap <- function(hs, palette = paletteer_d("ggsci::default_nejm" } print(module_to_col) print(col_mapping[order(names(col_mapping))]) + print(col_mapping) print(example_genes) modules = data.frame("module" = hs$modules) - modules$module = modules$module + modules$module = as.character(modules$module) ha = rowAnnotation(df = modules, col = col_mapping, simple_anno_size = unit(0.5, "in")) @@ -760,6 +762,6 @@ draw_hotspot_heatmap <- function(hs, palette = paletteer_d("ggsci::default_nejm" row_order = gene_order, column_order=gene_order, right_annotation=ha, column_names_gp = gpar(fontsize = c(1)), - width = unit(8, "in"), height = unit(8, "in")) + width = unit(5, "in"), height = unit(5, "in")) draw(ht) } diff --git a/vignettes/phyloVision.Rmd b/vignettes/phyloVision.Rmd index 7432613d..df59def2 100644 --- a/vignettes/phyloVision.Rmd +++ b/vignettes/phyloVision.Rmd @@ -67,12 +67,12 @@ vis <- analyzeHotspotObjectVision(vis, hs, tree=TRUE) ``` We can also access further Hotspot functionality using Reticulate and Python. -```{r inspectModules, eval=F} +```{r inspectModules, eval=T} hs <- loadHotspotObject(bytes=vis@Hotspot) library(reticulate) use_python('/usr/bin/python3') ``` -```{python modulesPlot, eval=F} +```{python modulesPlot, eval=T} import matplotlib.pyplot as plt import hotspot hs.plot_local_correlations() From 1ba5a45ea9427d186fd6210dd7ff1df8fb368c2e Mon Sep 17 00:00:00 2001 From: Yanay1 Date: Mon, 14 Jun 2021 22:10:03 -0700 Subject: [PATCH 46/62] updating docs --- docs/news/index.html | 6 +++--- docs/pkgdown.yml | 2 +- vignettes/phyloVision.Rmd | 4 ++-- 3 files changed, 6 insertions(+), 6 deletions(-) diff --git a/docs/news/index.html b/docs/news/index.html index 8183e9d8..f73d9388 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -160,9 +160,9 @@

Changelog

Source: NEWS.md -
-

-VISION 3.0

+
+

+VISION 3.0.0

Added support for Phylogenies as latent spaces in core VISION.

Integrated Hotspot into VISION analysis and report UI.

Deprecated support for trajectories and LC Annotator.

diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 176782f3..09b63f93 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -11,7 +11,7 @@ articles: web_only/10xData: 10xData.html web_only/Seurat: Seurat.html web_only/SignatureAutocorrelation: SignatureAutocorrelation.html -last_built: 2021-06-10T07:06Z +last_built: 2021-06-11T18:07Z urls: reference: https://yoseflab.github.io/VISION//reference article: https://yoseflab.github.io/VISION//articles diff --git a/vignettes/phyloVision.Rmd b/vignettes/phyloVision.Rmd index df59def2..7432613d 100644 --- a/vignettes/phyloVision.Rmd +++ b/vignettes/phyloVision.Rmd @@ -67,12 +67,12 @@ vis <- analyzeHotspotObjectVision(vis, hs, tree=TRUE) ``` We can also access further Hotspot functionality using Reticulate and Python. -```{r inspectModules, eval=T} +```{r inspectModules, eval=F} hs <- loadHotspotObject(bytes=vis@Hotspot) library(reticulate) use_python('/usr/bin/python3') ``` -```{python modulesPlot, eval=T} +```{python modulesPlot, eval=F} import matplotlib.pyplot as plt import hotspot hs.plot_local_correlations() From fbe1fea2c3d73f9056a553922524ea1c29834b4a Mon Sep 17 00:00:00 2001 From: Yanay1 Date: Wed, 16 Jun 2021 23:12:50 -0700 Subject: [PATCH 47/62] updating vignettes --- vignettes/spatialHotspot.Rmd | 47 +++++++++++++++++++++++++++++++++++- 1 file changed, 46 insertions(+), 1 deletion(-) diff --git a/vignettes/spatialHotspot.Rmd b/vignettes/spatialHotspot.Rmd index 7e8c3ef3..33ed37f0 100644 --- a/vignettes/spatialHotspot.Rmd +++ b/vignettes/spatialHotspot.Rmd @@ -7,7 +7,25 @@ vignette: > %\VignetteEngine{knitr::rmarkdown} %\VignetteEncoding{UTF-8} --- +# Preliminaries +If you have yet to install VISION, we recommend installing the package from Github to install this package. Full source code can be found at the VISION Github repository, available [here](http://www.github.com/YosefLab/VISION). + +```r +require(devtools) +install_github("YosefLab/VISION") +``` + +Once VISION and R are installed, you may load in VISION using `library(VISION)`. + +# Using VISION + +Running an analysis with vision consists of three steps: + +1. Creating the VISION object +2. Running the `analyze` function +3. Running Hotspot +3. Browsing results ```{r setup, include=FALSE} knitr::opts_chunk$set(echo = TRUE) @@ -37,6 +55,29 @@ pos <- pos[c("X", "Y")] # Construct the Vision object vis <- Vision(expr, signatures=c(sig), latentSpace = pos, meta=meta) # TODO add relevant signatures ``` +**Expression Data** + +The provided expression data should be scaled and normalized. It is recommended to apply more advanced normalization procedures such as batch correction or removal of technical confounders. + +The expression data should not be log-transformed prior to loading into VISION. + +**Signatures** + +Signatures can be provided as a list of paths to signature files (\*.gmt) or Signature objects. + +See [the signature vignette](Signatures.html) for more information on finding or creating gene Signatures. + +**Meta Data** + +An R data.frame with cell-level meta-data. This could be confounding variables (e.g. percentage of mitochondrial RNA, number of genes detected) or experimental covariates (e.g. genotype, donor, batch). + +This input is optional if Signatures are provided. + +**Other Options** + +Other options and inputs can be provided to customize how VISION runs. + +## Running an analysis Next, we can perform the normal Vision analysis using the spatial coordinates as the latent space. @@ -44,12 +85,16 @@ Next, we can perform the normal Vision analysis using the spatial coordinates as vis <- analyze(vis) ``` -We can also perform Hotspot module analysis. For more on the Hotspot API see [here](https://yoseflab.github.io/Hotspot/index.html) and the other included vignette. +## Running Hotpsot analysis + +We can also perform Hotspot module analysis. For more on the Hotspot API see [here](https://yoseflab.github.io/Hotspot/index.html) and [the PhyloVision vignette](phyloVision.html). ```{r hotspot, eval=F} vis@params$latentSpace$projectionGenes <- rownames(vis@exprData) # Use all genes. vis <- runHotspot(vis, model="bernoulli", num_umi=meta["num_umi"], logdata=FALSE) ``` + +## Viewing results Finally, we can launch the Vision browser. ```{r view, eval=F} viewResults(vis) From d738a29d8747cf3caa4f32703168f1943742f65a Mon Sep 17 00:00:00 2001 From: Yanay1 Date: Wed, 16 Jun 2021 23:13:01 -0700 Subject: [PATCH 48/62] updating vignettes --- vignettes/phyloVision.Rmd | 51 +++++++++++++++++++++++++++++++++++++++ 1 file changed, 51 insertions(+) diff --git a/vignettes/phyloVision.Rmd b/vignettes/phyloVision.Rmd index 7432613d..074d6942 100644 --- a/vignettes/phyloVision.Rmd +++ b/vignettes/phyloVision.Rmd @@ -8,6 +8,27 @@ vignette: > %\VignetteEncoding{UTF-8} --- +# Preliminaries + +If you have yet to install VISION, we recommend installing the package from Github to install this package. Full source code can be found at the VISION Github repository, available [here](http://www.github.com/YosefLab/VISION). + +```r +require(devtools) +install_github("YosefLab/VISION") +``` + +Once VISION and R are installed, you may load in VISION using `library(VISION)`. + +# Using PhyloVision + +Running an analysis with vision consists of three steps: + +1. Creating the PhyloVision object +2. Running the `phyloAnalyze` function +3. Running Hotspot +4. Browsing results + + ```{r setup, include=FALSE} knitr::opts_chunk$set(echo = TRUE) library(VISION) @@ -18,6 +39,7 @@ library(reticulate) ## Creating a PhyloVision Object with a Tree Vision objects now support dendrograms for visualization and analysis. To create the PhyloVision object, you need all of the same data, an expression matrix, and metadata and/or signatures, but you also include a tree object from the Ape package. + ```{r create, eval=F} # Read the expression and meta data file_path <- "data/embryogenesis" # Replace the path @@ -38,12 +60,40 @@ expr <- expr[, tree$tip.label] # Construct the Vision object vis <- PhyloVision(tree=tree, data=expr, signatures=sig, meta=meta, num_neighbors=30, projection_genes= rownames(expr)) ``` +**Tree** + +The `ape` phylogeny object. Singleton edges should be collapsed prior to use. The tree should be filtered to have the same cell (leaf) names as the expression data. + +**Expression Data** + +The provided expression data should be scaled and normalized. It is recommended to apply more advanced normalization procedures such as batch correction or removal of technical confounders. + +The expression data should not be log-transformed prior to loading into VISION. + +**Signatures** + +Signatures can be provided as a list of paths to signature files (\*.gmt) or Signature objects. + +See [the signature vignette](Signatures.html) for more information on finding or creating gene Signatures. + +**Meta Data** + +An R data.frame with cell-level meta-data. This could be confounding variables (e.g. percentage of mitochondrial RNA, number of genes detected) or experimental covariates (e.g. genotype, donor, batch). + +This input is optional if Signatures are provided. + +**Other Options** + +Other options and inputs can be provided to customize how VISION runs. + +## Running PhyloVision analysis Next, we can perform the normal Vision analysis using the tree as the latent space. ``` {r analyze, eval=F} vis <- phyloAnalyze(vis) ``` +## Running Hotpost analysis We can also perform Hotspot module analysis. The expression data is already logged for us. ```{r hotspot, eval=F} @@ -85,6 +135,7 @@ library(paletteer) draw_hotspot_heatmap(hs) ``` +## Viewing Results Finally, we can launch the Vision browser. ```{r eval=FALSE} From 11dab1abc9b7e59371b1194a649225cad4d4ad26 Mon Sep 17 00:00:00 2001 From: Yanay1 Date: Wed, 16 Jun 2021 23:15:53 -0700 Subject: [PATCH 49/62] updating news --- NEWS.md | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/NEWS.md b/NEWS.md index 6cfb87c6..7ada7135 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,10 +1,13 @@ # VISION 3.0.0 -Added support for Phylogenies as latent spaces in core VISION. +Major version bump! -Integrated [Hotspot](https://yoseflab.github.io/Hotspot/index.html) into VISION analysis and report UI. +* Added support for Phylogenies as latent spaces in core VISION and integrated with VISION api +* Re-engineered UI into Signature Autocorrelation and Hotspot views +* Integrated [Hotspot](https://yoseflab.github.io/Hotspot/index.html) into VISION analysis and report UI. +* Deprecated support for trajectories and LC Annotator. +* New color-scheme for gene expression values -Deprecated support for trajectories and LC Annotator. # VISION 2.1.0 From 1304d940e99441feb44db36c9681ec98daa85267 Mon Sep 17 00:00:00 2001 From: Yanay1 Date: Thu, 17 Jun 2021 01:16:00 -0700 Subject: [PATCH 50/62] cleaning up phyloplotly --- docs/articles/VISION-vignette.html | 4 +- docs/articles/trajectories.html | 4 +- docs/index.html | 4 +- docs/news/index.html | 11 +- docs/pkgdown.yml | 2 +- inst/html_output/src/PhyloPlotly.js | 238 ---------------------------- 6 files changed, 15 insertions(+), 248 deletions(-) diff --git a/docs/articles/VISION-vignette.html b/docs/articles/VISION-vignette.html index e9f01700..ff5473a5 100644 --- a/docs/articles/VISION-vignette.html +++ b/docs/articles/VISION-vignette.html @@ -129,8 +129,8 @@

Preliminaries

If you have yet to install VISION, we recommend installing the package from Github to install this package. Full source code can be found at the VISION Github repository, available here.

-require(devtools)
-install_github("YosefLab/VISION")
+require(devtools) +install_github("YosefLab/VISION")

Once VISION and R are installed, you may load in VISION using library(VISION).

diff --git a/docs/articles/trajectories.html b/docs/articles/trajectories.html index 2a3a6fe0..6a019dca 100644 --- a/docs/articles/trajectories.html +++ b/docs/articles/trajectories.html @@ -139,8 +139,8 @@

Installation

You should have a working installation of VISION, dyno, and tidyverse.

-devtools::install_github("YosefLab/VISION")
-devtools::install_github("dynverse/dyno")
+devtools::install_github("YosefLab/VISION")
+devtools::install_github("dynverse/dyno")
 install.packages('tidyverse')
diff --git a/docs/index.html b/docs/index.html index 2876beae..2e8bd33c 100644 --- a/docs/index.html +++ b/docs/index.html @@ -129,8 +129,8 @@

Installing VISION

We recommend installing VISION via github using devtools:

-library(devtools)
-install_github("YosefLab/VISION")
+library(devtools) +install_github("YosefLab/VISION")

See the DESCRIPTION file for a complete list of R dependencies. If the R dependencies are already installed, installation should finish in a few minutes.

diff --git a/docs/news/index.html b/docs/news/index.html index f73d9388..f07fa4ed 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -163,9 +163,14 @@

Changelog

VISION 3.0.0

-

Added support for Phylogenies as latent spaces in core VISION.

-

Integrated Hotspot into VISION analysis and report UI.

-

Deprecated support for trajectories and LC Annotator.

+

Major version bump!

+
    +
  • Added support for Phylogenies as latent spaces in core VISION and integrated with VISION api
    • +
  • Re-engineered UI into Signature Autocorrelation and Hotspot views
    • +
  • Integrated Hotspot into VISION analysis and report UI.
    • +
  • Deprecated support for trajectories and LC Annotator.
    • +
  • New color-scheme for gene expression values
    • +

diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 09b63f93..9dca1005 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -11,7 +11,7 @@ articles: web_only/10xData: 10xData.html web_only/Seurat: Seurat.html web_only/SignatureAutocorrelation: SignatureAutocorrelation.html -last_built: 2021-06-11T18:07Z +last_built: 2021-06-17T06:18Z urls: reference: https://yoseflab.github.io/VISION//reference article: https://yoseflab.github.io/VISION//articles diff --git a/inst/html_output/src/PhyloPlotly.js b/inst/html_output/src/PhyloPlotly.js index ac64ac95..9b0ffc96 100644 --- a/inst/html_output/src/PhyloPlotly.js +++ b/inst/html_output/src/PhyloPlotly.js @@ -846,241 +846,3 @@ function mode(arr) { return (Object.keys(freq).reduce((a, b) => freq[a] > freq[b] ? a : b)); } - - - -/* -function plotDendro(newick, div, radial, mapping, nodeColor) { - var tree = parseNewick(newick); - - function generatePlotlyData(collapsed) { - // treat collapsed nodes as leaves (special leaves though) - setUltrametricTreeDepths(tree, collapsed); - generateLinearCoords(tree); - - var x = []; - var y = []; - var names = []; - var colors = []; - var nodeSizes = []; - - var internalNodeSize = 5; - var tipSize = 6.3; - - function nodeCoords(tree) { - names.push(tree["name"]); - x.push(tree["x"]); - y.push(tree["y"]); - - if (collapsed.includes(tree["name"])) { - colors.push("#0000ff"); - nodeSizes.push(internalNodeSize); - // blue triangle for collapsed (color) - } else if (!isTip(tree)) { - colors.push("#a4a4a4"); - nodeSizes.push(internalNodeSize); - tree["branchset"].sort(function(a, b) {return a["depth"] - b["depth"]}).forEach(function(child) { - nodeCoords(child); - }); - } else { - nodeSizes.push(tipSize); - colors.push(nodeColor(mapping[tree["name"]])); - } - } - - nodeCoords(tree); - - - var yMin = Math.min(...y); - var yMax = Math.max(...y); - var d = 1; - - - - if (radial) { - x = []; - y = []; - colors = []; - nodeSizes = []; - function convertRadial(tree) { - var radialCoords = treeCordToRadial([tree["x"], tree["y"]]); - var coords = polorCoordToCartestian(radialCoords); - tree["r"] = radialCoords[0]; - tree["theta"] = radialCoords[1]; - tree["x"] = coords[0]; - tree["y"] = coords[1]; - x.push(coords[0]); - y.push(coords[1]); - if (collapsed.includes(tree["name"])) { - // collapsed - colors.push("#0000ff"); - nodeSizes.push(internalNodeSize); - } else if (!isTip(tree)) { - nodeSizes.push(internalNodeSize); - colors.push("#a4a4a4") - tree["branchset"].sort(function(a, b) {return a["depth"] - b["depth"]}).forEach(function(child) { - convertRadial(child); - }); - } else { - nodeSizes.push(tipSize); - colors.push(nodeColor(mapping[tree["name"]])); - } - } - - convertRadial(tree) - } - - - var xh = []; - var yh = []; - var xv = [] - var yv = []; - - if (radial) { - var rh = []; - var thetah = []; - var rv = [] - var thetav = []; - function lines(tree) { - if (!isTip(tree) && !collapsed.includes(tree["name"])) { - var rStart = tree["r"] - var theta = tree["theta"] - - var childrenRs = []; - var childrenThetas = []; - - tree["branchset"].sort(function(a, b) {return a["theta"] - b["theta"]}).forEach(function(child) { - lines(child); - childrenRs.push(child["r"]); - childrenThetas.push(child["theta"]); - }); - var rEnd = Math.min(...childrenRs); - var hlineEnd = (rStart + rEnd)/2; - - rh = rh.concat([rStart, hlineEnd, null]) // first part of connection, x - thetah = thetah.concat([theta, theta, null]) // first part of connection, y - - - // draw the second parts horizontal x - childrenRs.forEach(function(r) { - rh = rh.concat([hlineEnd, r, null]); - }); - - // draw the second parts horizontal y - childrenThetas.forEach(function(theta) { - thetah = thetah.concat([theta, theta, null]) - }) - - // draw the vertical part as a spline - var maxTheta = Math.max(...childrenThetas); - var minTheta = Math.min(...childrenThetas); - var thetaRange = _.range(minTheta, maxTheta, (maxTheta - minTheta)/25) - childrenThetas.concat([theta]).concat(thetaRange).sort().forEach(function(thetaC) { - rv.push(hlineEnd); - thetav.push(thetaC); - }) - - rv.push(null); - thetav.push(null); - - } - } - - lines(tree) - - var coords = _.unzip(_.zip(rh, thetah).map(polorCoordToCartestian)) - xh = coords[0]; - yh = coords[1]; - coords = _.unzip(_.zip(rv, thetav).map(polorCoordToCartestian)) - xv = coords[0]; - yv = coords[1]; - - } else { - function lines(tree) { - if (!isTip(tree) && !collapsed.includes(tree["name"])) { - var xStart = tree["x"] - var y = tree["y"] - - var childrenXs = []; - var childrenYs = [] - tree["branchset"].sort(function(a, b) {return a["depth"] - b["depth"]}).forEach(function(child) { - lines(child); - childrenXs.push(child["x"]); - childrenYs.push(child["y"]); - }); - var xEnd = Math.min(...childrenXs); - var hlineEnd = (xStart + xEnd)/2; - xh = xh.concat([xStart, hlineEnd, null]) // first part of connection, x - yh = yh.concat([y, y, null]) // first part of connection, y - - // draw the second parts horizontal x - childrenXs.forEach(function(x) { - xh = xh.concat([hlineEnd, x, null]); - }); - - // draw the second parts horizontal y - childrenYs.forEach(function(y) { - yh = yh.concat([y, y, null]) - }) - - // draw the vertical part - xv = xv.concat([hlineEnd, hlineEnd, null]); - yv = yv.concat([Math.min(...childrenYs), Math.max(...childrenYs), null]); - } - } - lines(tree) - } - - var nodesTrace = { - x: x, - y: y, - type: "scattergl", - text: names, - mode: "markers", - marker: { - color: colors, - size: nodeSizes, - opacity: 1 - }, - hoverinfo: "text" - - } - - var horizontalLines = { - x: xh, - y: yh, - mode: "lines", - type:"scatter", - line: { - color: '#000000', - width: 0.5, - shape: "spline" - }, - hoverinfo: 'skip' - } - - var verticalLines = { - x: xv, - y: yv, - mode: "lines", - type:"scatter", - line: { - color: '#000000', - width: 0.5, - shape: "spline" - }, - hoverinfo: 'skip' - } - return([horizontalLines, verticalLines, nodesTrace]); - } - - - - - - var data = generatePlotlyData([]); - // clear any existing event listeners - - return({"tree": tree, "data": data, "layout": layout}) -} -*/ From 19f69bbfd7c4be69c073635e88bde314e5d0f14c Mon Sep 17 00:00:00 2001 From: Yanay1 Date: Thu, 17 Jun 2021 10:57:40 -0700 Subject: [PATCH 51/62] adding imports to vignettes --- docs/pkgdown.yml | 2 +- vignettes/phyloVision.Rmd | 6 +++--- vignettes/spatialHotspot.Rmd | 3 ++- 3 files changed, 6 insertions(+), 5 deletions(-) diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 9dca1005..06f1087d 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -11,7 +11,7 @@ articles: web_only/10xData: 10xData.html web_only/Seurat: Seurat.html web_only/SignatureAutocorrelation: SignatureAutocorrelation.html -last_built: 2021-06-17T06:18Z +last_built: 2021-06-17T17:55Z urls: reference: https://yoseflab.github.io/VISION//reference article: https://yoseflab.github.io/VISION//articles diff --git a/vignettes/phyloVision.Rmd b/vignettes/phyloVision.Rmd index 074d6942..8e92eb91 100644 --- a/vignettes/phyloVision.Rmd +++ b/vignettes/phyloVision.Rmd @@ -28,12 +28,12 @@ Running an analysis with vision consists of three steps: 3. Running Hotspot 4. Browsing results - -```{r setup, include=FALSE} +First, we need to load VISION, reticulate and ape. +```{r setup, eval=F} knitr::opts_chunk$set(echo = TRUE) library(VISION) -library(ape) library(reticulate) +library(ape) ``` ## Creating a PhyloVision Object with a Tree diff --git a/vignettes/spatialHotspot.Rmd b/vignettes/spatialHotspot.Rmd index 33ed37f0..2c422a55 100644 --- a/vignettes/spatialHotspot.Rmd +++ b/vignettes/spatialHotspot.Rmd @@ -27,7 +27,8 @@ Running an analysis with vision consists of three steps: 3. Running Hotspot 3. Browsing results -```{r setup, include=FALSE} +First, we need to load VISION and reticulate. +```{r setup, eval=F} knitr::opts_chunk$set(echo = TRUE) library(VISION) library(reticulate) From 8ab6e29e596e811d8bfa7158a4c5a9da3c15d88a Mon Sep 17 00:00:00 2001 From: Yanay1 Date: Tue, 27 Jul 2021 11:59:34 -0700 Subject: [PATCH 52/62] fixed whitelist and overflow --- inst/html_output/Results.html | 6 ++---- inst/html_output/whitelist.txt | 4 +--- 2 files changed, 3 insertions(+), 7 deletions(-) diff --git a/inst/html_output/Results.html b/inst/html_output/Results.html index 6fcb2cc3..76b07170 100644 --- a/inst/html_output/Results.html +++ b/inst/html_output/Results.html @@ -11,7 +11,6 @@ - @@ -24,7 +23,6 @@ - @@ -107,8 +105,8 @@

-
-
+
+
diff --git a/inst/html_output/whitelist.txt b/inst/html_output/whitelist.txt index 8c9ec40f..ca37a9e5 100644 --- a/inst/html_output/whitelist.txt +++ b/inst/html_output/whitelist.txt @@ -36,6 +36,4 @@ html_output/thirdparty/jszip/jszip.min.js html_output/thirdparty/lodash/lodash.min.js html_output/thirdparty/plotly/plotly.js-1.45.2/dist/plotly.min.js html_output/thirdparty/popper/popper.js/dist/umd/popper.min.js -html_output/thirdparty/hsluv/hsluv-0.1.0.min.js -html_output/thirdparty/phylotree/phylotree.js -html_output/thirdparty/phylotree/phylotree.css \ No newline at end of file +html_output/thirdparty/hsluv/hsluv-0.1.0.min.js \ No newline at end of file From 5c00ade7f3325f71f0ed0d660ad40b51d7910c01 Mon Sep 17 00:00:00 2001 From: Yanay1 Date: Mon, 16 Aug 2021 11:53:49 -0700 Subject: [PATCH 53/62] updating docs --- docs/404.html | 194 +++++++++++++ .../empty-anchor.js | 15 + .../header-attrs-2.8/header-attrs.js | 12 + .../empty-anchor.js | 15 + .../header-attrs-2.8/header-attrs.js | 12 + .../empty-anchor.js | 15 + .../header-attrs-2.8/header-attrs.js | 12 + docs/articles/phyloVision.html | 266 +++++++++++++++++ .../empty-anchor.js | 15 + .../header-attrs-2.8/header-attrs.js | 12 + docs/articles/spatialHotspot.html | 235 +++++++++++++++ .../empty-anchor.js | 15 + .../header-attrs-2.8/header-attrs.js | 12 + .../empty-anchor.js | 15 + .../header-attrs-2.8/header-attrs.js | 12 + .../empty-anchor.js | 15 + .../header-attrs-2.8/header-attrs.js | 12 + .../empty-anchor.js | 15 + .../header-attrs-2.8/header-attrs.js | 12 + .../empty-anchor.js | 15 + .../header-attrs-2.8/header-attrs.js | 12 + docs/bootstrap-toc.css | 60 ++++ docs/bootstrap-toc.js | 159 +++++++++++ docs/reference/PhyloVision-class.html | 215 ++++++++++++++ docs/reference/addHotspotToVision.html | 215 ++++++++++++++ .../reference/analyzeHotspotObjectVision.html | 232 +++++++++++++++ .../analyzeLocalCorrelationsModules.html | 221 +++++++++++++++ docs/reference/ancestor_at_depth.html | 219 ++++++++++++++ docs/reference/calcModuleScores.html | 226 +++++++++++++++ docs/reference/calc_mod_sig_enrichment.html | 215 ++++++++++++++ docs/reference/calc_set_enrichment.html | 229 +++++++++++++++ docs/reference/clusterModScores.html | 215 ++++++++++++++ .../computeKNNWeights-phylo-method.html | 230 +++++++++++++++ .../depthBasedCladewiseTreeCluster.html | 221 +++++++++++++++ docs/reference/depthBasedTreeCluster.html | 221 +++++++++++++++ docs/reference/draw_hotspot_heatmap.html | 212 ++++++++++++++ docs/reference/find_knn_parallel_tree.html | 221 +++++++++++++++ docs/reference/find_root.html | 211 ++++++++++++++ docs/reference/generateOverlapSignatures.html | 211 ++++++++++++++ docs/reference/get_all_children.html | 215 ++++++++++++++ docs/reference/get_children.html | 215 ++++++++++++++ docs/reference/get_max_cluster_size.html | 215 ++++++++++++++ docs/reference/get_min_cluster_size.html | 215 ++++++++++++++ docs/reference/get_parent.html | 215 ++++++++++++++ docs/reference/group_modules_enrichment.html | 225 +++++++++++++++ docs/reference/hsCalculateModuleScores.html | 229 +++++++++++++++ docs/reference/hsComputeAutoCorrelations.html | 223 +++++++++++++++ .../reference/hsComputeLocalCorrelations.html | 220 ++++++++++++++ docs/reference/hsCreateKnnGraph.html | 203 +++++++++++++ docs/reference/hsInit.html | 227 +++++++++++++++ docs/reference/is_tip.html | 215 ++++++++++++++ docs/reference/knn_tree.html | 225 +++++++++++++++ docs/reference/lcaBasedHotspotNeighbors.html | 208 ++++++++++++++ docs/reference/lcaBasedTreeKNN.html | 206 ++++++++++++++ docs/reference/lca_based_depth.html | 219 ++++++++++++++ docs/reference/loadHotspotObject.html | 215 ++++++++++++++ .../maxSizeCladewiseTreeCluster.html | 221 +++++++++++++++ docs/reference/minSizeCladeNeighbors.html | 219 ++++++++++++++ .../phyloAnalyze-PhyloVision-method.html | 209 ++++++++++++++ docs/reference/runHotspot.html | 268 ++++++++++++++++++ docs/reference/saveHSBytestToPickle.html | 212 ++++++++++++++ docs/reference/treeClusterMinCladeSize.html | 216 ++++++++++++++ docs/reference/trivial_dist.html | 221 +++++++++++++++ docs/reference/ultrametric_tree.html | 211 ++++++++++++++ man/PhyloVision-class.Rd | 19 ++ man/addHotspotToVision.Rd | 19 ++ man/analyzeHotspotObjectVision.Rd | 28 ++ man/analyzeLocalCorrelationsModules.Rd | 22 ++ man/ancestor_at_depth.Rd | 21 ++ man/calcModuleScores.Rd | 27 ++ man/calc_mod_sig_enrichment.Rd | 19 ++ man/calc_set_enrichment.Rd | 25 ++ man/clusterModScores.Rd | 19 ++ man/computeKNNWeights-phylo-method.Rd | 31 ++ man/depthBasedCladewiseTreeCluster.Rd | 22 ++ man/depthBasedTreeCluster.Rd | 22 ++ man/draw_hotspot_heatmap.Rd | 16 ++ man/find_knn_parallel_tree.Rd | 23 ++ man/find_root.Rd | 17 ++ man/generateOverlapSignatures.Rd | 17 ++ man/get_all_children.Rd | 19 ++ man/get_children.Rd | 19 ++ man/get_max_cluster_size.Rd | 19 ++ man/get_min_cluster_size.Rd | 19 ++ man/get_parent.Rd | 19 ++ man/group_modules_enrichment.Rd | 23 ++ man/hsCalculateModuleScores.Rd | 28 ++ man/hsComputeAutoCorrelations.Rd | 25 ++ man/hsComputeLocalCorrelations.Rd | 21 ++ man/hsCreateKnnGraph.Rd | 14 + man/hsInit.Rd | 25 ++ man/is_tip.Rd | 19 ++ man/knn_tree.Rd | 25 ++ man/lcaBasedHotspotNeighbors.Rd | 16 ++ man/lcaBasedTreeKNN.Rd | 14 + man/lca_based_depth.Rd | 21 ++ man/loadHotspotObject.Rd | 19 ++ man/maxSizeCladewiseTreeCluster.Rd | 22 ++ man/minSizeCladeNeighbors.Rd | 21 ++ man/phyloAnalyze-PhyloVision-method.Rd | 15 + man/runHotspot.Rd | 56 ++++ man/saveHSBytestToPickle.Rd | 16 ++ man/treeClusterMinCladeSize.Rd | 20 ++ man/trivial_dist.Rd | 22 ++ man/ultrametric_tree.Rd | 17 ++ 105 files changed, 11019 insertions(+) create mode 100644 docs/404.html create mode 100644 docs/articles/Signatures_files/accessible-code-block-0.0.1/empty-anchor.js create mode 100644 docs/articles/Signatures_files/header-attrs-2.8/header-attrs.js create mode 100644 docs/articles/VISION-vignette_files/accessible-code-block-0.0.1/empty-anchor.js create 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docs/reference/calcModuleScores.html create mode 100644 docs/reference/calc_mod_sig_enrichment.html create mode 100644 docs/reference/calc_set_enrichment.html create mode 100644 docs/reference/clusterModScores.html create mode 100644 docs/reference/computeKNNWeights-phylo-method.html create mode 100644 docs/reference/depthBasedCladewiseTreeCluster.html create mode 100644 docs/reference/depthBasedTreeCluster.html create mode 100644 docs/reference/draw_hotspot_heatmap.html create mode 100644 docs/reference/find_knn_parallel_tree.html create mode 100644 docs/reference/find_root.html create mode 100644 docs/reference/generateOverlapSignatures.html create mode 100644 docs/reference/get_all_children.html create mode 100644 docs/reference/get_children.html create mode 100644 docs/reference/get_max_cluster_size.html create mode 100644 docs/reference/get_min_cluster_size.html create mode 100644 docs/reference/get_parent.html create mode 100644 docs/reference/group_modules_enrichment.html create mode 100644 docs/reference/hsCalculateModuleScores.html create mode 100644 docs/reference/hsComputeAutoCorrelations.html create mode 100644 docs/reference/hsComputeLocalCorrelations.html create mode 100644 docs/reference/hsCreateKnnGraph.html create mode 100644 docs/reference/hsInit.html create mode 100644 docs/reference/is_tip.html create mode 100644 docs/reference/knn_tree.html create mode 100644 docs/reference/lcaBasedHotspotNeighbors.html create mode 100644 docs/reference/lcaBasedTreeKNN.html create mode 100644 docs/reference/lca_based_depth.html create mode 100644 docs/reference/loadHotspotObject.html create mode 100644 docs/reference/maxSizeCladewiseTreeCluster.html create mode 100644 docs/reference/minSizeCladeNeighbors.html create mode 100644 docs/reference/phyloAnalyze-PhyloVision-method.html create mode 100644 docs/reference/runHotspot.html create mode 100644 docs/reference/saveHSBytestToPickle.html create mode 100644 docs/reference/treeClusterMinCladeSize.html create mode 100644 docs/reference/trivial_dist.html create mode 100644 docs/reference/ultrametric_tree.html create mode 100644 man/PhyloVision-class.Rd create mode 100644 man/addHotspotToVision.Rd create mode 100644 man/analyzeHotspotObjectVision.Rd create mode 100644 man/analyzeLocalCorrelationsModules.Rd create mode 100644 man/ancestor_at_depth.Rd create mode 100644 man/calcModuleScores.Rd create mode 100644 man/calc_mod_sig_enrichment.Rd create mode 100644 man/calc_set_enrichment.Rd create mode 100644 man/clusterModScores.Rd create mode 100644 man/computeKNNWeights-phylo-method.Rd create mode 100644 man/depthBasedCladewiseTreeCluster.Rd create mode 100644 man/depthBasedTreeCluster.Rd create mode 100644 man/draw_hotspot_heatmap.Rd create mode 100644 man/find_knn_parallel_tree.Rd create mode 100644 man/find_root.Rd create mode 100644 man/generateOverlapSignatures.Rd create mode 100644 man/get_all_children.Rd create mode 100644 man/get_children.Rd create mode 100644 man/get_max_cluster_size.Rd create mode 100644 man/get_min_cluster_size.Rd create mode 100644 man/get_parent.Rd create mode 100644 man/group_modules_enrichment.Rd create mode 100644 man/hsCalculateModuleScores.Rd create mode 100644 man/hsComputeAutoCorrelations.Rd create mode 100644 man/hsComputeLocalCorrelations.Rd create mode 100644 man/hsCreateKnnGraph.Rd create mode 100644 man/hsInit.Rd create mode 100644 man/is_tip.Rd create mode 100644 man/knn_tree.Rd create mode 100644 man/lcaBasedHotspotNeighbors.Rd create mode 100644 man/lcaBasedTreeKNN.Rd create mode 100644 man/lca_based_depth.Rd create mode 100644 man/loadHotspotObject.Rd create mode 100644 man/maxSizeCladewiseTreeCluster.Rd create mode 100644 man/minSizeCladeNeighbors.Rd create mode 100644 man/phyloAnalyze-PhyloVision-method.Rd create mode 100644 man/runHotspot.Rd create mode 100644 man/saveHSBytestToPickle.Rd create mode 100644 man/treeClusterMinCladeSize.Rd create mode 100644 man/trivial_dist.Rd create mode 100644 man/ultrametric_tree.Rd diff --git a/docs/404.html b/docs/404.html new file mode 100644 index 00000000..945dddb6 --- /dev/null +++ b/docs/404.html @@ -0,0 +1,194 @@ + + + + + + + + +Page not found (404) • VISION + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+
+ + + + +
+ +
+
+
+

Page not found (404)

+
+ +Content not found. Please use links in the navbar. + +
+ + + +
+ + + +
+
+

Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

+
+ +
+

Site built with pkgdown 1.6.1.

+
+ +
+
+ + + + + + + + diff --git a/docs/articles/Signatures_files/accessible-code-block-0.0.1/empty-anchor.js b/docs/articles/Signatures_files/accessible-code-block-0.0.1/empty-anchor.js new file mode 100644 index 00000000..ca349fd6 --- /dev/null +++ b/docs/articles/Signatures_files/accessible-code-block-0.0.1/empty-anchor.js @@ -0,0 +1,15 @@ +// Hide empty tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) --> +// v0.0.1 +// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020. + +document.addEventListener('DOMContentLoaded', function() { + const codeList = document.getElementsByClassName("sourceCode"); + for (var i = 0; i < codeList.length; i++) { + var linkList = codeList[i].getElementsByTagName('a'); + for (var j = 0; j < linkList.length; j++) { + if (linkList[j].innerHTML === "") { + linkList[j].setAttribute('aria-hidden', 'true'); + } + } + } +}); diff --git a/docs/articles/Signatures_files/header-attrs-2.8/header-attrs.js b/docs/articles/Signatures_files/header-attrs-2.8/header-attrs.js new file mode 100644 index 00000000..dd57d92e --- /dev/null +++ b/docs/articles/Signatures_files/header-attrs-2.8/header-attrs.js @@ -0,0 +1,12 @@ +// Pandoc 2.9 adds attributes on both header and div. We remove the former (to +// be compatible with the behavior of Pandoc < 2.8). +document.addEventListener('DOMContentLoaded', function(e) { + var hs = document.querySelectorAll("div.section[class*='level'] > :first-child"); + var i, h, a; + for (i = 0; i < hs.length; i++) { + h = hs[i]; + if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6 + a = h.attributes; + while (a.length > 0) h.removeAttribute(a[0].name); + } +}); diff --git a/docs/articles/VISION-vignette_files/accessible-code-block-0.0.1/empty-anchor.js b/docs/articles/VISION-vignette_files/accessible-code-block-0.0.1/empty-anchor.js new file mode 100644 index 00000000..ca349fd6 --- /dev/null +++ b/docs/articles/VISION-vignette_files/accessible-code-block-0.0.1/empty-anchor.js @@ -0,0 +1,15 @@ +// Hide empty tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) --> +// v0.0.1 +// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020. + +document.addEventListener('DOMContentLoaded', function() { + const codeList = document.getElementsByClassName("sourceCode"); + for (var i = 0; i < codeList.length; i++) { + var linkList = codeList[i].getElementsByTagName('a'); + for (var j = 0; j < linkList.length; j++) { + if (linkList[j].innerHTML === "") { + linkList[j].setAttribute('aria-hidden', 'true'); + } + } + } +}); diff --git a/docs/articles/VISION-vignette_files/header-attrs-2.8/header-attrs.js b/docs/articles/VISION-vignette_files/header-attrs-2.8/header-attrs.js new file mode 100644 index 00000000..dd57d92e --- /dev/null +++ b/docs/articles/VISION-vignette_files/header-attrs-2.8/header-attrs.js @@ -0,0 +1,12 @@ +// Pandoc 2.9 adds attributes on both header and div. We remove the former (to +// be compatible with the behavior of Pandoc < 2.8). +document.addEventListener('DOMContentLoaded', function(e) { + var hs = document.querySelectorAll("div.section[class*='level'] > :first-child"); + var i, h, a; + for (i = 0; i < hs.length; i++) { + h = hs[i]; + if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6 + a = h.attributes; + while (a.length > 0) h.removeAttribute(a[0].name); + } +}); diff --git a/docs/articles/micropooling_files/accessible-code-block-0.0.1/empty-anchor.js b/docs/articles/micropooling_files/accessible-code-block-0.0.1/empty-anchor.js new file mode 100644 index 00000000..ca349fd6 --- /dev/null +++ b/docs/articles/micropooling_files/accessible-code-block-0.0.1/empty-anchor.js @@ -0,0 +1,15 @@ +// Hide empty tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) --> +// v0.0.1 +// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020. + +document.addEventListener('DOMContentLoaded', function() { + const codeList = document.getElementsByClassName("sourceCode"); + for (var i = 0; i < codeList.length; i++) { + var linkList = codeList[i].getElementsByTagName('a'); + for (var j = 0; j < linkList.length; j++) { + if (linkList[j].innerHTML === "") { + linkList[j].setAttribute('aria-hidden', 'true'); + } + } + } +}); diff --git a/docs/articles/micropooling_files/header-attrs-2.8/header-attrs.js b/docs/articles/micropooling_files/header-attrs-2.8/header-attrs.js new file mode 100644 index 00000000..dd57d92e --- /dev/null +++ b/docs/articles/micropooling_files/header-attrs-2.8/header-attrs.js @@ -0,0 +1,12 @@ +// Pandoc 2.9 adds attributes on both header and div. We remove the former (to +// be compatible with the behavior of Pandoc < 2.8). +document.addEventListener('DOMContentLoaded', function(e) { + var hs = document.querySelectorAll("div.section[class*='level'] > :first-child"); + var i, h, a; + for (i = 0; i < hs.length; i++) { + h = hs[i]; + if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6 + a = h.attributes; + while (a.length > 0) h.removeAttribute(a[0].name); + } +}); diff --git a/docs/articles/phyloVision.html b/docs/articles/phyloVision.html new file mode 100644 index 00000000..3eaf50b4 --- /dev/null +++ b/docs/articles/phyloVision.html @@ -0,0 +1,266 @@ + + + + + + + +Introduction to PhyloVision and Hotspot • VISION + + + + + + + + + + + + + + + + + + +
+
+ + + + +
+
+
+

Introduction to PhyloVision and Hotspot

+ + + Source: vignettes/phyloVision.Rmd + + +
+ + + +
+

+Preliminaries

+

If you have yet to install VISION, we recommend installing the package from Github to install this package. Full source code can be found at the VISION Github repository, available here.

+
+require(devtools)
+install_github("YosefLab/VISION")
+

Once VISION and R are installed, you may load in VISION using library(VISION).

+
+
+

+Using PhyloVision

+

Running an analysis with vision consists of three steps:

+
    +
  1. Creating the PhyloVision object
    2. +
  2. Running the phyloAnalyze function
    3. +
  3. Running Hotspot
    4. +
  4. Browsing results
    5. +
+

First, we need to load VISION, reticulate and ape.

+
+knitr::opts_chunk$set(echo = TRUE)
+library(VISION)
+library(reticulate)
+library(ape)
+
+

+Creating a PhyloVision Object with a Tree

+

Vision objects now support dendrograms for visualization and analysis. To create the PhyloVision object, you need all of the same data, an expression matrix, and metadata and/or signatures, but you also include a tree object from the Ape package.

+
+# Read the expression and meta data
+file_path <- "data/embryogenesis" # Replace the path
+
+expr <- read.table(paste(file_path, "expr_filtered.tsv.gz", sep="/"), check.names = FALSE, sep = "\t")
+
+meta <- read.table(paste(file_path, "meta.tsv", sep="/"), check.names = FALSE, sep = "\t", row.names = 1, header=TRUE)
+meta$Cell_Type <- as.factor(meta$Cell_Type)
+# Signature file
+sig <- paste("data", "h.all.v5.2.symbols.gmt", sep="/")
+
+# Read the tree
+tree <- read.tree(paste(file_path, "embryo_tree.newick", sep="/"))
+# Collapse one mutations
+tree <- collapse.singles(tree)
+expr <- expr[, tree$tip.label]
+
+# Construct the Vision object
+vis <- PhyloVision(tree=tree, data=expr, signatures=sig, meta=meta, num_neighbors=30, projection_genes= rownames(expr))
+

Tree

+

The ape phylogeny object. Singleton edges should be collapsed prior to use. The tree should be filtered to have the same cell (leaf) names as the expression data.

+

Expression Data

+

The provided expression data should be scaled and normalized. It is recommended to apply more advanced normalization procedures such as batch correction or removal of technical confounders.

+

The expression data should not be log-transformed prior to loading into VISION.

+

Signatures

+

Signatures can be provided as a list of paths to signature files (*.gmt) or Signature objects.

+

See the signature vignette for more information on finding or creating gene Signatures.

+

Meta Data

+

An R data.frame with cell-level meta-data. This could be confounding variables (e.g. percentage of mitochondrial RNA, number of genes detected) or experimental covariates (e.g. genotype, donor, batch).

+

This input is optional if Signatures are provided.

+

Other Options

+

Other options and inputs can be provided to customize how VISION runs.

+
+
+

+Running PhyloVision analysis

+

Next, we can perform the normal Vision analysis using the tree as the latent space.

+
+vis <- phyloAnalyze(vis)
+
+
+

+Running Hotpost analysis

+

We can also perform Hotspot module analysis. The expression data is already logged for us.

+
+vis <- runHotspot(vis, model="normal", tree=TRUE, min_gene_threshold=50, n_neighbors = 30, number_top_genes = nrow(expr), logdata=FALSE)
+

The full Hotspot API is exposed for analysis as well. For more on the Hotspot API see here

+
+# Init Hotspot
+hs <- hsInit(vis, model = "normal", tree=TRUE, logdata=FALSE)
+# Init Hotspot KNN
+hs <- hsCreateKnnGraph(hs, vis, n_neighbors=30)
+# perform Hotspot analysis and store results in R
+hs_genes <- hsComputeAutoCorrelations(hs, number_top_genes=12438)
+# Compute localcorr
+hs <- hsComputeLocalCorrelations(hs, hs_genes)
+# Calculate Hotspot Module Scores for informative genes
+hs <- hsCalculateModuleScores(hs)
+# Cluster Hotspot modules and perform Vision based analysis on HS Modules and 
+vis <- analyzeHotspotObjectVision(vis, hs, tree=TRUE)
+

We can also access further Hotspot functionality using Reticulate and Python.

+
+hs <- loadHotspotObject(bytes=vis@Hotspot)
+library(reticulate)
+use_python('/usr/bin/python3')
+
import matplotlib.pyplot as plt
+import hotspot
+hs.plot_local_correlations()
+plt.show()
+

Note: the heatmap can also be visualized like so:

+
+hs <- loadHotspotObject(bytes=vis@Hotspot)
+library(paletteer)
+draw_hotspot_heatmap(hs)
+
+
+

+Viewing Results

+

Finally, we can launch the Vision browser.

+ +
+
+
+ + + +
+ + + +
+

Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

+
+ +
+

Site built with pkgdown 1.6.1.

+
+ +
+
+ + + + + + diff --git a/docs/articles/phyloVision_files/accessible-code-block-0.0.1/empty-anchor.js b/docs/articles/phyloVision_files/accessible-code-block-0.0.1/empty-anchor.js new file mode 100644 index 00000000..ca349fd6 --- /dev/null +++ b/docs/articles/phyloVision_files/accessible-code-block-0.0.1/empty-anchor.js @@ -0,0 +1,15 @@ +// Hide empty tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) --> +// v0.0.1 +// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020. + +document.addEventListener('DOMContentLoaded', function() { + const codeList = document.getElementsByClassName("sourceCode"); + for (var i = 0; i < codeList.length; i++) { + var linkList = codeList[i].getElementsByTagName('a'); + for (var j = 0; j < linkList.length; j++) { + if (linkList[j].innerHTML === "") { + linkList[j].setAttribute('aria-hidden', 'true'); + } + } + } +}); diff --git a/docs/articles/phyloVision_files/header-attrs-2.8/header-attrs.js b/docs/articles/phyloVision_files/header-attrs-2.8/header-attrs.js new file mode 100644 index 00000000..dd57d92e --- /dev/null +++ b/docs/articles/phyloVision_files/header-attrs-2.8/header-attrs.js @@ -0,0 +1,12 @@ +// Pandoc 2.9 adds attributes on both header and div. We remove the former (to +// be compatible with the behavior of Pandoc < 2.8). +document.addEventListener('DOMContentLoaded', function(e) { + var hs = document.querySelectorAll("div.section[class*='level'] > :first-child"); + var i, h, a; + for (i = 0; i < hs.length; i++) { + h = hs[i]; + if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6 + a = h.attributes; + while (a.length > 0) h.removeAttribute(a[0].name); + } +}); diff --git a/docs/articles/spatialHotspot.html b/docs/articles/spatialHotspot.html new file mode 100644 index 00000000..3f265304 --- /dev/null +++ b/docs/articles/spatialHotspot.html @@ -0,0 +1,235 @@ + + + + + + + +Spatial Data and Hotspot • VISION + + + + + + + + + + + + + + + + + + +
+
+ + + + +
+
+
+

Spatial Data and Hotspot

+ + + Source: vignettes/spatialHotspot.Rmd + + +
+ + + +
+

+Preliminaries

+

If you have yet to install VISION, we recommend installing the package from Github to install this package. Full source code can be found at the VISION Github repository, available here.

+
+require(devtools)
+install_github("YosefLab/VISION")
+

Once VISION and R are installed, you may load in VISION using library(VISION).

+
+
+

+Using VISION

+

Running an analysis with vision consists of three steps:

+
    +
  1. Creating the VISION object
    2. +
  2. Running the analyze function
    3. +
  3. Running Hotspot
    4. +
  4. Browsing results
    5. +
+

First, we need to load VISION and reticulate.

+
+knitr::opts_chunk$set(echo = TRUE)
+library(VISION)
+library(reticulate)
+
+

+Creating a Vision Object

+

First, we create a Vision object

+
+# Read the expression and meta data
+file_path <- "data/spatial" # Replace the path
+
+expr <- read.table(paste(file_path, "expr.tsv.gz", sep="/"), check.names = FALSE, sep = "\t")
+meta <- read.table(paste(file_path, "meta.tsv", sep="/"), check.names = FALSE, sep = "\t", row.names = 1, header=TRUE)
+
+# Signature file
+sig <- paste("data", "h.all.v5.2.symbols.gmt", sep="/")
+
+# Read and create the coordinates
+pos <- read.table(paste(file_path, "BeadLocationsForR.csv", sep="/"), sep=",", check.names = FALSE, row.names=1, header=TRUE)
+pos["X"] <- pos$ycoord
+pos["Y"] <- -1 * pos$xcoord
+pos <- pos[c("X", "Y")]
+
+# Construct the Vision object
+vis <- Vision(expr, signatures=c(sig), latentSpace = pos, meta=meta) # TODO add relevant signatures
+

Expression Data

+

The provided expression data should be scaled and normalized. It is recommended to apply more advanced normalization procedures such as batch correction or removal of technical confounders.

+

The expression data should not be log-transformed prior to loading into VISION.

+

Signatures

+

Signatures can be provided as a list of paths to signature files (*.gmt) or Signature objects.

+

See the signature vignette for more information on finding or creating gene Signatures.

+

Meta Data

+

An R data.frame with cell-level meta-data. This could be confounding variables (e.g. percentage of mitochondrial RNA, number of genes detected) or experimental covariates (e.g. genotype, donor, batch).

+

This input is optional if Signatures are provided.

+

Other Options

+

Other options and inputs can be provided to customize how VISION runs.

+
+
+

+Running an analysis

+

Next, we can perform the normal Vision analysis using the spatial coordinates as the latent space.

+
+vis <- analyze(vis)
+
+
+

+Running Hotpsot analysis

+

We can also perform Hotspot module analysis. For more on the Hotspot API see here and the PhyloVision vignette.

+
+vis@params$latentSpace$projectionGenes <- rownames(vis@exprData) # Use all genes.
+vis <- runHotspot(vis, model="bernoulli", num_umi=meta["num_umi"], logdata=FALSE)
+
+
+

+Viewing results

+

Finally, we can launch the Vision browser.

+ +
+
+
+ + + +
+ + + +
+

Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

+
+ +
+

Site built with pkgdown 1.6.1.

+
+ +
+
+ + + + + + diff --git a/docs/articles/spatialHotspot_files/accessible-code-block-0.0.1/empty-anchor.js b/docs/articles/spatialHotspot_files/accessible-code-block-0.0.1/empty-anchor.js new file mode 100644 index 00000000..ca349fd6 --- /dev/null +++ b/docs/articles/spatialHotspot_files/accessible-code-block-0.0.1/empty-anchor.js @@ -0,0 +1,15 @@ +// Hide empty tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) --> +// v0.0.1 +// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020. + +document.addEventListener('DOMContentLoaded', function() { + const codeList = document.getElementsByClassName("sourceCode"); + for (var i = 0; i < codeList.length; i++) { + var linkList = codeList[i].getElementsByTagName('a'); + for (var j = 0; j < linkList.length; j++) { + if (linkList[j].innerHTML === "") { + linkList[j].setAttribute('aria-hidden', 'true'); + } + } + } +}); diff --git a/docs/articles/spatialHotspot_files/header-attrs-2.8/header-attrs.js b/docs/articles/spatialHotspot_files/header-attrs-2.8/header-attrs.js new file mode 100644 index 00000000..dd57d92e --- /dev/null +++ b/docs/articles/spatialHotspot_files/header-attrs-2.8/header-attrs.js @@ -0,0 +1,12 @@ +// Pandoc 2.9 adds attributes on both header and div. We remove the former (to +// be compatible with the behavior of Pandoc < 2.8). +document.addEventListener('DOMContentLoaded', function(e) { + var hs = document.querySelectorAll("div.section[class*='level'] > :first-child"); + var i, h, a; + for (i = 0; i < hs.length; i++) { + h = hs[i]; + if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6 + a = h.attributes; + while (a.length > 0) h.removeAttribute(a[0].name); + } +}); diff --git a/docs/articles/trajectories_files/accessible-code-block-0.0.1/empty-anchor.js b/docs/articles/trajectories_files/accessible-code-block-0.0.1/empty-anchor.js new file mode 100644 index 00000000..ca349fd6 --- /dev/null +++ b/docs/articles/trajectories_files/accessible-code-block-0.0.1/empty-anchor.js @@ -0,0 +1,15 @@ +// Hide empty tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) --> +// v0.0.1 +// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020. + +document.addEventListener('DOMContentLoaded', function() { + const codeList = document.getElementsByClassName("sourceCode"); + for (var i = 0; i < codeList.length; i++) { + var linkList = codeList[i].getElementsByTagName('a'); + for (var j = 0; j < linkList.length; j++) { + if (linkList[j].innerHTML === "") { + linkList[j].setAttribute('aria-hidden', 'true'); + } + } + } +}); diff --git a/docs/articles/trajectories_files/header-attrs-2.8/header-attrs.js b/docs/articles/trajectories_files/header-attrs-2.8/header-attrs.js new file mode 100644 index 00000000..dd57d92e --- /dev/null +++ b/docs/articles/trajectories_files/header-attrs-2.8/header-attrs.js @@ -0,0 +1,12 @@ +// Pandoc 2.9 adds attributes on both header and div. We remove the former (to +// be compatible with the behavior of Pandoc < 2.8). +document.addEventListener('DOMContentLoaded', function(e) { + var hs = document.querySelectorAll("div.section[class*='level'] > :first-child"); + var i, h, a; + for (i = 0; i < hs.length; i++) { + h = hs[i]; + if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6 + a = h.attributes; + while (a.length > 0) h.removeAttribute(a[0].name); + } +}); diff --git a/docs/articles/web_only/10xData_files/accessible-code-block-0.0.1/empty-anchor.js b/docs/articles/web_only/10xData_files/accessible-code-block-0.0.1/empty-anchor.js new file mode 100644 index 00000000..ca349fd6 --- /dev/null +++ b/docs/articles/web_only/10xData_files/accessible-code-block-0.0.1/empty-anchor.js @@ -0,0 +1,15 @@ +// Hide empty tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) --> +// v0.0.1 +// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020. + +document.addEventListener('DOMContentLoaded', function() { + const codeList = document.getElementsByClassName("sourceCode"); + for (var i = 0; i < codeList.length; i++) { + var linkList = codeList[i].getElementsByTagName('a'); + for (var j = 0; j < linkList.length; j++) { + if (linkList[j].innerHTML === "") { + linkList[j].setAttribute('aria-hidden', 'true'); + } + } + } +}); diff --git a/docs/articles/web_only/10xData_files/header-attrs-2.8/header-attrs.js b/docs/articles/web_only/10xData_files/header-attrs-2.8/header-attrs.js new file mode 100644 index 00000000..dd57d92e --- /dev/null +++ b/docs/articles/web_only/10xData_files/header-attrs-2.8/header-attrs.js @@ -0,0 +1,12 @@ +// Pandoc 2.9 adds attributes on both header and div. We remove the former (to +// be compatible with the behavior of Pandoc < 2.8). +document.addEventListener('DOMContentLoaded', function(e) { + var hs = document.querySelectorAll("div.section[class*='level'] > :first-child"); + var i, h, a; + for (i = 0; i < hs.length; i++) { + h = hs[i]; + if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6 + a = h.attributes; + while (a.length > 0) h.removeAttribute(a[0].name); + } +}); diff --git a/docs/articles/web_only/Seurat_files/accessible-code-block-0.0.1/empty-anchor.js b/docs/articles/web_only/Seurat_files/accessible-code-block-0.0.1/empty-anchor.js new file mode 100644 index 00000000..ca349fd6 --- /dev/null +++ b/docs/articles/web_only/Seurat_files/accessible-code-block-0.0.1/empty-anchor.js @@ -0,0 +1,15 @@ +// Hide empty tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) --> +// v0.0.1 +// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020. + +document.addEventListener('DOMContentLoaded', function() { + const codeList = document.getElementsByClassName("sourceCode"); + for (var i = 0; i < codeList.length; i++) { + var linkList = codeList[i].getElementsByTagName('a'); + for (var j = 0; j < linkList.length; j++) { + if (linkList[j].innerHTML === "") { + linkList[j].setAttribute('aria-hidden', 'true'); + } + } + } +}); diff --git a/docs/articles/web_only/Seurat_files/header-attrs-2.8/header-attrs.js b/docs/articles/web_only/Seurat_files/header-attrs-2.8/header-attrs.js new file mode 100644 index 00000000..dd57d92e --- /dev/null +++ b/docs/articles/web_only/Seurat_files/header-attrs-2.8/header-attrs.js @@ -0,0 +1,12 @@ +// Pandoc 2.9 adds attributes on both header and div. We remove the former (to +// be compatible with the behavior of Pandoc < 2.8). +document.addEventListener('DOMContentLoaded', function(e) { + var hs = document.querySelectorAll("div.section[class*='level'] > :first-child"); + var i, h, a; + for (i = 0; i < hs.length; i++) { + h = hs[i]; + if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6 + a = h.attributes; + while (a.length > 0) h.removeAttribute(a[0].name); + } +}); diff --git a/docs/articles/web_only/SignatureAutocorrelation_files/accessible-code-block-0.0.1/empty-anchor.js b/docs/articles/web_only/SignatureAutocorrelation_files/accessible-code-block-0.0.1/empty-anchor.js new file mode 100644 index 00000000..ca349fd6 --- /dev/null +++ b/docs/articles/web_only/SignatureAutocorrelation_files/accessible-code-block-0.0.1/empty-anchor.js @@ -0,0 +1,15 @@ +// Hide empty tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) --> +// v0.0.1 +// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020. + +document.addEventListener('DOMContentLoaded', function() { + const codeList = document.getElementsByClassName("sourceCode"); + for (var i = 0; i < codeList.length; i++) { + var linkList = codeList[i].getElementsByTagName('a'); + for (var j = 0; j < linkList.length; j++) { + if (linkList[j].innerHTML === "") { + linkList[j].setAttribute('aria-hidden', 'true'); + } + } + } +}); diff --git a/docs/articles/web_only/SignatureAutocorrelation_files/header-attrs-2.8/header-attrs.js b/docs/articles/web_only/SignatureAutocorrelation_files/header-attrs-2.8/header-attrs.js new file mode 100644 index 00000000..dd57d92e --- /dev/null +++ b/docs/articles/web_only/SignatureAutocorrelation_files/header-attrs-2.8/header-attrs.js @@ -0,0 +1,12 @@ +// Pandoc 2.9 adds attributes on both header and div. We remove the former (to +// be compatible with the behavior of Pandoc < 2.8). +document.addEventListener('DOMContentLoaded', function(e) { + var hs = document.querySelectorAll("div.section[class*='level'] > :first-child"); + var i, h, a; + for (i = 0; i < hs.length; i++) { + h = hs[i]; + if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6 + a = h.attributes; + while (a.length > 0) h.removeAttribute(a[0].name); + } +}); diff --git a/docs/bootstrap-toc.css b/docs/bootstrap-toc.css new file mode 100644 index 00000000..5a859415 --- /dev/null +++ b/docs/bootstrap-toc.css @@ -0,0 +1,60 @@ +/*! + * Bootstrap Table of Contents v0.4.1 (http://afeld.github.io/bootstrap-toc/) + * Copyright 2015 Aidan Feldman + * Licensed under MIT (https://github.com/afeld/bootstrap-toc/blob/gh-pages/LICENSE.md) */ + +/* modified from https://github.com/twbs/bootstrap/blob/94b4076dd2efba9af71f0b18d4ee4b163aa9e0dd/docs/assets/css/src/docs.css#L548-L601 */ + +/* All levels of nav */ +nav[data-toggle='toc'] .nav > li > a { + display: block; + padding: 4px 20px; + font-size: 13px; + font-weight: 500; + color: #767676; +} +nav[data-toggle='toc'] .nav > li > a:hover, +nav[data-toggle='toc'] .nav > li > a:focus { + padding-left: 19px; + color: #563d7c; + text-decoration: none; + background-color: transparent; + border-left: 1px solid #563d7c; +} +nav[data-toggle='toc'] .nav > .active > a, +nav[data-toggle='toc'] .nav > .active:hover > a, +nav[data-toggle='toc'] .nav > .active:focus > a { + padding-left: 18px; + font-weight: bold; + color: #563d7c; + background-color: transparent; + border-left: 2px solid #563d7c; +} + +/* Nav: second level (shown on .active) */ +nav[data-toggle='toc'] .nav .nav { + display: none; /* Hide by default, but at >768px, show it */ + padding-bottom: 10px; +} +nav[data-toggle='toc'] .nav .nav > li > a { + padding-top: 1px; + padding-bottom: 1px; + padding-left: 30px; + font-size: 12px; + font-weight: normal; +} +nav[data-toggle='toc'] .nav .nav > li > a:hover, +nav[data-toggle='toc'] .nav .nav > li > a:focus { + padding-left: 29px; +} +nav[data-toggle='toc'] .nav .nav > .active > a, +nav[data-toggle='toc'] .nav .nav > .active:hover > a, +nav[data-toggle='toc'] .nav .nav > .active:focus > a { + padding-left: 28px; + font-weight: 500; +} + +/* from https://github.com/twbs/bootstrap/blob/e38f066d8c203c3e032da0ff23cd2d6098ee2dd6/docs/assets/css/src/docs.css#L631-L634 */ +nav[data-toggle='toc'] .nav > .active > ul { + display: block; +} diff --git a/docs/bootstrap-toc.js b/docs/bootstrap-toc.js new file mode 100644 index 00000000..1cdd573b --- /dev/null +++ b/docs/bootstrap-toc.js @@ -0,0 +1,159 @@ +/*! + * Bootstrap Table of Contents v0.4.1 (http://afeld.github.io/bootstrap-toc/) + * Copyright 2015 Aidan Feldman + * Licensed under MIT (https://github.com/afeld/bootstrap-toc/blob/gh-pages/LICENSE.md) */ +(function() { + 'use strict'; + + window.Toc = { + helpers: { + // return all matching elements in the set, or their descendants + findOrFilter: function($el, selector) { + // http://danielnouri.org/notes/2011/03/14/a-jquery-find-that-also-finds-the-root-element/ + // http://stackoverflow.com/a/12731439/358804 + var $descendants = $el.find(selector); + return $el.filter(selector).add($descendants).filter(':not([data-toc-skip])'); + }, + + generateUniqueIdBase: function(el) { + var text = $(el).text(); + var anchor = text.trim().toLowerCase().replace(/[^A-Za-z0-9]+/g, '-'); + return anchor || el.tagName.toLowerCase(); + }, + + generateUniqueId: function(el) { + var anchorBase = this.generateUniqueIdBase(el); + for (var i = 0; ; i++) { + var anchor = anchorBase; + if (i > 0) { + // add suffix + anchor += '-' + i; + } + // check if ID already exists + if (!document.getElementById(anchor)) { + return anchor; + } + } + }, + + generateAnchor: function(el) { + if (el.id) { + return el.id; + } else { + var anchor = this.generateUniqueId(el); + el.id = anchor; + return anchor; + } + }, + + createNavList: function() { + return $('
    '); + }, + + createChildNavList: function($parent) { + var $childList = this.createNavList(); + $parent.append($childList); + return $childList; + }, + + generateNavEl: function(anchor, text) { + var $a = $('    '); + $a.attr('href', '#' + anchor); + $a.text(text); + var $li = $('
  • '); + $li.append($a); + return $li; + }, + + generateNavItem: function(headingEl) { + var anchor = this.generateAnchor(headingEl); + var $heading = $(headingEl); + var text = $heading.data('toc-text') || $heading.text(); + return this.generateNavEl(anchor, text); + }, + + // Find the first heading level (`

    `, then `

    `, etc.) that has more than one element. Defaults to 1 (for `

    `). + getTopLevel: function($scope) { + for (var i = 1; i <= 6; i++) { + var $headings = this.findOrFilter($scope, 'h' + i); + if ($headings.length > 1) { + return i; + } + } + + return 1; + }, + + // returns the elements for the top level, and the next below it + getHeadings: function($scope, topLevel) { + var topSelector = 'h' + topLevel; + + var secondaryLevel = topLevel + 1; + var secondarySelector = 'h' + secondaryLevel; + + return this.findOrFilter($scope, topSelector + ',' + secondarySelector); + }, + + getNavLevel: function(el) { + return parseInt(el.tagName.charAt(1), 10); + }, + + populateNav: function($topContext, topLevel, $headings) { + var $context = $topContext; + var $prevNav; + + var helpers = this; + $headings.each(function(i, el) { + var $newNav = helpers.generateNavItem(el); + var navLevel = helpers.getNavLevel(el); + + // determine the proper $context + if (navLevel === topLevel) { + // use top level + $context = $topContext; + } else if ($prevNav && $context === $topContext) { + // create a new level of the tree and switch to it + $context = helpers.createChildNavList($prevNav); + } // else use the current $context + + $context.append($newNav); + + $prevNav = $newNav; + }); + }, + + parseOps: function(arg) { + var opts; + if (arg.jquery) { + opts = { + $nav: arg + }; + } else { + opts = arg; + } + opts.$scope = opts.$scope || $(document.body); + return opts; + } + }, + + // accepts a jQuery object, or an options object + init: function(opts) { + opts = this.helpers.parseOps(opts); + + // ensure that the data attribute is in place for styling + opts.$nav.attr('data-toggle', 'toc'); + + var $topContext = this.helpers.createChildNavList(opts.$nav); + var topLevel = this.helpers.getTopLevel(opts.$scope); + var $headings = this.helpers.getHeadings(opts.$scope, topLevel); + this.helpers.populateNav($topContext, topLevel, $headings); + } + }; + + $(function() { + $('nav[data-toggle="toc"]').each(function(i, el) { + var $nav = $(el); + Toc.init($nav); + }); + }); +})(); diff --git a/docs/reference/PhyloVision-class.html b/docs/reference/PhyloVision-class.html new file mode 100644 index 00000000..012d26d8 --- /dev/null +++ b/docs/reference/PhyloVision-class.html @@ -0,0 +1,215 @@ + + + + + + + + +Initializes a new PhyloVision Object — PhyloVision • VISION + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + + +
    + +
    +
    +
    +

    Initializes a new PhyloVision Object

    + Source: R/AllGenerics.R, R/methods-Vision.R + +
    + +
    +

    Initializes a new PhyloVision Object

    +
    + + 
    PhyloVision(tree, ...)
+
+# S4 method for phylo
+PhyloVision(tree, ...)
    + +

    Arguments

    +

    + + + + + + + + + +
    tree

    parsed ape tree

    ...

    arguments passed to the base Vision constructor

    + + +
    + +
    + + +
    +
    +

    Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

    +
    + +
    +

    Site built with pkgdown 1.6.1.

    +
    + +
    +
    + + + + + + + + diff --git a/docs/reference/addHotspotToVision.html b/docs/reference/addHotspotToVision.html new file mode 100644 index 00000000..30873b22 --- /dev/null +++ b/docs/reference/addHotspotToVision.html @@ -0,0 +1,215 @@ + + + + + + + + +Add HS python obj to vision OBJECT — addHotspotToVision • VISION + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + + +
    + +
    +
    +
    +

    Add HS python obj to vision OBJECT

    + Source: R/methods-Module.R + +
    + +
    +

    Add HS python obj to vision OBJECT

    +
    + + 
    addHotspotToVision(object, hs)
    + +

    Arguments

    + + + + + + + + + + +
    object

    Vision object

    hs

    python hs object

    + +

    Value

    + +

    Vision object with hs populated

    + +
    + +
    + + +
    +
    +

    Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

    +
    + +
    +

    Site built with pkgdown 1.6.1.

    +
    + +
    +
    + + + + + + + + diff --git a/docs/reference/analyzeHotspotObjectVision.html b/docs/reference/analyzeHotspotObjectVision.html new file mode 100644 index 00000000..67674a73 --- /dev/null +++ b/docs/reference/analyzeHotspotObjectVision.html @@ -0,0 +1,232 @@ + + + + + + + + +Analyze a Hotspot object using built in methods such +such as local correlation, signature overlap, etc. +Necessary to run this function for Hotspot functionality in viewer to work. — analyzeHotspotObjectVision • VISION + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + + +
    + +
    +
    +
    +

    Analyze a Hotspot object using built in methods such +such as local correlation, signature overlap, etc. +Necessary to run this function for Hotspot functionality in viewer to work.

    + Source: R/methods-Module.R + +
    + +
    +

    Analyze a Hotspot object using built in methods such +such as local correlation, signature overlap, etc. +Necessary to run this function for Hotspot functionality in viewer to work.

    +
    + + 
    analyzeHotspotObjectVision(object, hs, tree = FALSE)
    + +

    Arguments

    + + + + + + + + + + + + + + +
    object

    the VISION object

    hs

    the Hotspot python object loaded by Reticulate

    tree

    whether to use tree as latent space. If TRUE, object should have a tree

    + +

    Value

    + +

    the modified VISION object with the following slots filled: +Populates the modData, HotspotModuleScores, ModuleSignatureEnrichment +and HotspotObject slots of object, as well as recalculates signature scores +for new modules.

    + +
    + +
    + + +
    +
    +

    Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

    +
    + +
    +

    Site built with pkgdown 1.6.1.

    +
    + +
    +
    + + + + + + + + diff --git a/docs/reference/analyzeLocalCorrelationsModules.html b/docs/reference/analyzeLocalCorrelationsModules.html new file mode 100644 index 00000000..c294bb50 --- /dev/null +++ b/docs/reference/analyzeLocalCorrelationsModules.html @@ -0,0 +1,221 @@ + + + + + + + + +Compute local correlations for all modules — analyzeLocalCorrelationsModules • VISION + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + + +
    + +
    +
    +
    +

    Compute local correlations for all modules

    + Source: R/methods-Module.R + +
    + +
    +

    This is the main analysis function. For each filtered dataset, a set of +different projection onto low-dimensional space are computed, and the +consistency of the resulting space with the signature scores is computed +to find signals that are captured successfully by the projections.

    +
    + + 
    analyzeLocalCorrelationsModules(object, tree = FALSE)
    + +

    Arguments

    + + + + + + + + + + +
    object

    the VISION object

    tree

    whether to use the tree object as latent space for neighbors

    + +

    Value

    + +

    the VISION object with values set for the analysis results

    + +
    + +
    + + +
    +
    +

    Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

    +
    + +
    +

    Site built with pkgdown 1.6.1.

    +
    + +
    +
    + + + + + + + + diff --git a/docs/reference/ancestor_at_depth.html b/docs/reference/ancestor_at_depth.html new file mode 100644 index 00000000..6a85ddbb --- /dev/null +++ b/docs/reference/ancestor_at_depth.html @@ -0,0 +1,219 @@ + + + + + + + + +Find the ancestor of a node above a specific depth — ancestor_at_depth • VISION + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + + +
    + +
    +
    +
    +

    Find the ancestor of a node above a specific depth

    + Source: R/Utilities.R + +
    + +
    +

    Find the ancestor of a node above a specific depth

    +
    + + 
    ancestor_at_depth(tree, node, depth)
    + +

    Arguments

    + + + + + + + + + + + + + + +
    tree

    an object of class phylo

    node

    the index of the node

    depth

    the depth to search to

    + +

    Value

    + +

    the index of the ancestor node

    + +
    + +
    + + +
    +
    +

    Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

    +
    + +
    +

    Site built with pkgdown 1.6.1.

    +
    + +
    +
    + + + + + + + + diff --git a/docs/reference/calcModuleScores.html b/docs/reference/calcModuleScores.html new file mode 100644 index 00000000..c463159f --- /dev/null +++ b/docs/reference/calcModuleScores.html @@ -0,0 +1,226 @@ + + + + + + + + +Calculate module scores (signature scores but on the modules) — calcModuleScores • VISION + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + + +
    + +
    +
    +
    +

    Calculate module scores (signature scores but on the modules)

    + Source: R/methods-Module.R + +
    + +
    +

    For each module-cell pair, compute a score that captures the level of +correspondence between the cell and the module.

    +
    + + 
    calcModuleScores(object, mod_norm_method = NULL, mod_gene_importance = TRUE)
    + +

    Arguments

    + + + + + + + + + + + + + + +
    object

    the VISION object

    mod_norm_method

    Method to apply to normalize the expression matrix +before calculating signature scores. Valid options are: +"znorm_columns" (default), "none", "znorm_rows", "znorm_rows_then_columns", +or "rank_norm_columns"

    mod_gene_importance

    whether or not to rank each gene's contribution to +the overall signature score. Default = TRUE. This is used for inspecting +genes in a signature in the output report

    + +

    Value

    + +

    the VISION object, with the @ModScores and @ModGeneImportance slots populated

    + +
    + +
    + + +
    +
    +

    Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

    +
    + +
    +

    Site built with pkgdown 1.6.1.

    +
    + +
    +
    + + + + + + + + diff --git a/docs/reference/calc_mod_sig_enrichment.html b/docs/reference/calc_mod_sig_enrichment.html new file mode 100644 index 00000000..eed30fac --- /dev/null +++ b/docs/reference/calc_mod_sig_enrichment.html @@ -0,0 +1,215 @@ + + + + + + + + +Computes the hypergeometric overlap test for modules and signatures — calc_mod_sig_enrichment • VISION + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + + +
    + +
    +
    +
    +

    Computes the hypergeometric overlap test for modules and signatures

    + Source: R/methods-Module.R + +
    + +
    +

    Computes the hypergeometric overlap test for modules and signatures

    +
    + + 
    calc_mod_sig_enrichment(object, skip_down = TRUE)
    + +

    Arguments

    + + + + + + + + + + +
    object

    the Vision object.

    skip_down

    whether to ignore down signatures in overlap

    + +

    Value

    + +

    list(statistic values, p values, clusters of signatures)

    + +
    + +
    + + +
    +
    +

    Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

    +
    + +
    +

    Site built with pkgdown 1.6.1.

    +
    + +
    +
    + + + + + + + + diff --git a/docs/reference/calc_set_enrichment.html b/docs/reference/calc_set_enrichment.html new file mode 100644 index 00000000..cbf8978f --- /dev/null +++ b/docs/reference/calc_set_enrichment.html @@ -0,0 +1,229 @@ + + + + + + + + +Calculate the hypergeometric enrichment for two sets from a population +Statisic = log (observed overlap / expected overlap) +P value = 1- hypergeometric(observed overlap -1, max(|set1|, |set2|), |genes| - |set1|, min(|set1|, |set2|)) — calc_set_enrichment • VISION + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + + +
    + +
    +
    +
    +

    Calculate the hypergeometric enrichment for two sets from a population +Statisic = log (observed overlap / expected overlap) +P value = 1- hypergeometric(observed overlap -1, max(|set1|, |set2|), |genes| - |set1|, min(|set1|, |set2|))

    + Source: R/methods-Module.R + +
    + +
    +

    Calculate the hypergeometric enrichment for two sets from a population +Statisic = log (observed overlap / expected overlap) +P value = 1- hypergeometric(observed overlap -1, max(|set1|, |set2|), |genes| - |set1|, min(|set1|, |set2|))

    +
    + + 
    calc_set_enrichment(set1, set2, genes)
    + +

    Arguments

    + + + + + + + + + + + + + + +
    set1

    the first gene set

    set2

    the second gene set

    genes

    the population

    + +

    Value

    + +

    c(statistic, p value)

    + +
    + +
    + + +
    +
    +

    Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

    +
    + +
    +

    Site built with pkgdown 1.6.1.

    +
    + +
    +
    + + + + + + + + diff --git a/docs/reference/clusterModScores.html b/docs/reference/clusterModScores.html new file mode 100644 index 00000000..b5b26422 --- /dev/null +++ b/docs/reference/clusterModScores.html @@ -0,0 +1,215 @@ + + + + + + + + +Compute Ranksums Test, for all factor meta data. One level vs all others — clusterModScores • VISION + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + + +
    + +
    +
    +
    +

    Compute Ranksums Test, for all factor meta data. One level vs all others

    + Source: R/methods-Module.R + +
    + +
    +

    Compute Ranksums Test, for all factor meta data. One level vs all others

    +
    + + 
    clusterModScores(object, variables = "All")
    + +

    Arguments

    + + + + + + + + + + +
    object

    the VISION object

    variables

    which columns of the meta-data to use for comparisons

    + +

    Value

    + +

    the VISION object with the @ClusterComparisons modules slot populated

    + +
    + +
    + + +
    +
    +

    Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

    +
    + +
    +

    Site built with pkgdown 1.6.1.

    +
    + +
    +
    + + + + + + + + diff --git a/docs/reference/computeKNNWeights-phylo-method.html b/docs/reference/computeKNNWeights-phylo-method.html new file mode 100644 index 00000000..4861a703 --- /dev/null +++ b/docs/reference/computeKNNWeights-phylo-method.html @@ -0,0 +1,230 @@ + + + + + + + + +Compute for each vector the weights to apply to it's K nearest neighbors — computeKNNWeights,phylo-method • VISION + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + + +
    + +
    +
    +
    +

    Compute for each vector the weights to apply to it's K nearest neighbors

    + Source: R/Projections.R + +
    + +
    +

    Compute for each vector the weights to apply to it's K nearest neighbors

    +
    + + 
    # S4 method for phylo
+computeKNNWeights(
+  object,
+  K = round(sqrt(length(object$tip.label))),
+  lcaKNN = FALSE,
+  minSize = 20
+)
    + +

    Arguments

    + + + + + + + + + + + + + + +
    object

    tree to use for KNN

    K

    Number of neighbors to consider.

    lcaKNN

    whether to use LCA based KNN (cluster by minimum size), if false defaults to cophenetic distance (random tie breaking). +WARNING: lcaKNN doesn't perform well with broad multifurcations

    + +

    Value

    + +

    a list of two items: + indices: matrix, cells X neighbors + Each row specifies indices of nearest neighbors + weights: matrix, cells X neighbors + Corresponding weights to nearest neighbors

    + +
    + +
    + + +
    +
    +

    Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

    +
    + +
    +

    Site built with pkgdown 1.6.1.

    +
    + +
    +
    + + + + + + + + diff --git a/docs/reference/depthBasedCladewiseTreeCluster.html b/docs/reference/depthBasedCladewiseTreeCluster.html new file mode 100644 index 00000000..7aee7cee --- /dev/null +++ b/docs/reference/depthBasedCladewiseTreeCluster.html @@ -0,0 +1,221 @@ + + + + + + + + +Performs a breadth first search to create a specific number of clusters. +Clusters are split based on depth. — depthBasedCladewiseTreeCluster • VISION + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + + +
    + +
    +
    +
    +

    Performs a breadth first search to create a specific number of clusters. +Clusters are split based on depth.

    + Source: R/Microclusters.R + +
    + +
    +

    Performs a breadth first search to create a specific number of clusters. +Clusters are split based on depth.

    +
    + + 
    depthBasedCladewiseTreeCluster(tree, target = 10)
    + +

    Arguments

    + + + + + + + + + + +
    tree

    object of class phylo

    target

    number of clusters to attempt to generate

    + +

    Value

    + +

    List of clusters, each entry being a vector of indices representing +samples in the cluster.

    + +
    + +
    + + +
    +
    +

    Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

    +
    + +
    +

    Site built with pkgdown 1.6.1.

    +
    + +
    +
    + + + + + + + + diff --git a/docs/reference/depthBasedTreeCluster.html b/docs/reference/depthBasedTreeCluster.html new file mode 100644 index 00000000..9134f6d3 --- /dev/null +++ b/docs/reference/depthBasedTreeCluster.html @@ -0,0 +1,221 @@ + + + + + + + + +Performs a binary search on a depth d such that +if depth(LCA(u, v)) <= d then u and v are in the same cluster — depthBasedTreeCluster • VISION + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + + +
    + +
    +
    +
    +

    Performs a binary search on a depth d such that +if depth(LCA(u, v)) <= d then u and v are in the same cluster

    + Source: R/Microclusters.R + +
    + +
    +

    Performs a binary search on a depth d such that +if depth(LCA(u, v)) <= d then u and v are in the same cluster

    +
    + + 
    depthBasedTreeCluster(tree, target = 10)
    + +

    Arguments

    + + + + + + + + + + +
    tree

    object of class phylo

    target

    number of clusters to attempt to generate

    + +

    Value

    + +

    List of clusters, each entry being a vector of indices representing +samples in the cluster.

    + +
    + +
    + + +
    +
    +

    Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

    +
    + +
    +

    Site built with pkgdown 1.6.1.

    +
    + +
    +
    + + + + + + + + diff --git a/docs/reference/draw_hotspot_heatmap.html b/docs/reference/draw_hotspot_heatmap.html new file mode 100644 index 00000000..6c8475bf --- /dev/null +++ b/docs/reference/draw_hotspot_heatmap.html @@ -0,0 +1,212 @@ + + + + + + + + +Draw Modules Heatmap (Gene x Gene) — draw_hotspot_heatmap • VISION + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + + +
    + +
    +
    +
    +

    Draw Modules Heatmap (Gene x Gene)

    + Source: R/methods-Module.R + +
    + +
    +

    Draw Modules Heatmap (Gene x Gene)

    +
    + + 
    draw_hotspot_heatmap(hs, palette = paletteer_d("ggsci::default_nejm"))
    + +

    Arguments

    + + + + + + + + + + +
    hs

    the Hotspot Object

    palette

    palette

    + + +
    + +
    + + +
    +
    +

    Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

    +
    + +
    +

    Site built with pkgdown 1.6.1.

    +
    + +
    +
    + + + + + + + + diff --git a/docs/reference/find_knn_parallel_tree.html b/docs/reference/find_knn_parallel_tree.html new file mode 100644 index 00000000..81c839e2 --- /dev/null +++ b/docs/reference/find_knn_parallel_tree.html @@ -0,0 +1,221 @@ + + + + + + + + +Parallel KNN for Trees — find_knn_parallel_tree • VISION + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + + +
    + +
    +
    +
    +

    Parallel KNN for Trees

    + Source: R/Utilities.R + +
    + +
    +

    Computes nearest-neighbor indices and distances +in parallel. Query is over all points and results +do not include the self-distance.

    +
    + + 
    find_knn_parallel_tree(tree, K)
    + +

    Arguments

    + + + + + + + + + + +
    tree

    an object of class phylo

    K

    number of neighbors to query

    + +

    Value

    + +

    list with two items: + index: Samples x K matrix of neighbor indices + dist: Samples x K matrix of neighbor distances

    + +
    + +
    + + +
    +
    +

    Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

    +
    + +
    +

    Site built with pkgdown 1.6.1.

    +
    + +
    +
    + + + + + + + + diff --git a/docs/reference/find_root.html b/docs/reference/find_root.html new file mode 100644 index 00000000..b057e4e3 --- /dev/null +++ b/docs/reference/find_root.html @@ -0,0 +1,211 @@ + + + + + + + + +Find the root node — find_root • VISION + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + + +
    + +
    +
    +
    +

    Find the root node

    + Source: R/Utilities.R + +
    + +
    +

    Find the root node

    +
    + + 
    find_root(tree)
    + +

    Arguments

    + + + + + + +
    tree

    an object of class phylo

    + +

    Value

    + +

    the index of the root node

    + +
    + +
    + + +
    +
    +

    Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

    +
    + +
    +

    Site built with pkgdown 1.6.1.

    +
    + +
    +
    + + + + + + + + diff --git a/docs/reference/generateOverlapSignatures.html b/docs/reference/generateOverlapSignatures.html new file mode 100644 index 00000000..d2b5fe8f --- /dev/null +++ b/docs/reference/generateOverlapSignatures.html @@ -0,0 +1,211 @@ + + + + + + + + +Generates signature objects for the overlap sets between modules and signatures — generateOverlapSignatures • VISION + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + + +
    + +
    +
    +
    +

    Generates signature objects for the overlap sets between modules and signatures

    + Source: R/methods-Module.R + +
    + +
    +

    Generates signature objects for the overlap sets between modules and signatures

    +
    + + 
    generateOverlapSignatures(object)
    + +

    Arguments

    + + + + + + +
    object

    the Vision object

    + +

    Value

    + +

    Vision Object, populates the modData slot with overlap signatures.

    + +
    + +
    + + +
    +
    +

    Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

    +
    + +
    +

    Site built with pkgdown 1.6.1.

    +
    + +
    +
    + + + + + + + + diff --git a/docs/reference/get_all_children.html b/docs/reference/get_all_children.html new file mode 100644 index 00000000..c9b5b8f5 --- /dev/null +++ b/docs/reference/get_all_children.html @@ -0,0 +1,215 @@ + + + + + + + + +Get all the tip children of a node. — get_all_children • VISION + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + + +
    + +
    +
    +
    +

    Get all the tip children of a node.

    + Source: R/Utilities.R + +
    + +
    +

    Get all the tip children of a node.

    +
    + + 
    get_all_children(tree, node)
    + +

    Arguments

    + + + + + + + + + + +
    tree

    an object of class phylo

    node

    the node to check

    + +

    Value

    + +

    the tips

    + +
    + +
    + + +
    +
    +

    Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

    +
    + +
    +

    Site built with pkgdown 1.6.1.

    +
    + +
    +
    + + + + + + + + diff --git a/docs/reference/get_children.html b/docs/reference/get_children.html new file mode 100644 index 00000000..d67de3bc --- /dev/null +++ b/docs/reference/get_children.html @@ -0,0 +1,215 @@ + + + + + + + + +Find the children of a node — get_children • VISION + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + + +
    + +
    +
    +
    +

    Find the children of a node

    + Source: R/Utilities.R + +
    + +
    +

    Find the children of a node

    +
    + + 
    get_children(tree, node)
    + +

    Arguments

    + + + + + + + + + + +
    tree

    an object of class phylo

    node

    the node to get the children of

    + +

    Value

    + +

    the children

    + +
    + +
    + + +
    +
    +

    Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

    +
    + +
    +

    Site built with pkgdown 1.6.1.

    +
    + +
    +
    + + + + + + + + diff --git a/docs/reference/get_max_cluster_size.html b/docs/reference/get_max_cluster_size.html new file mode 100644 index 00000000..8a351371 --- /dev/null +++ b/docs/reference/get_max_cluster_size.html @@ -0,0 +1,215 @@ + + + + + + + + +Tree method for getting the max child clade size of a node — get_max_cluster_size • VISION + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + + +
    + +
    +
    +
    +

    Tree method for getting the max child clade size of a node

    + Source: R/Utilities.R + +
    + +
    +

    Tree method for getting the max child clade size of a node

    +
    + + 
    get_max_cluster_size(tree, node)
    + +

    Arguments

    + + + + + + + + + + +
    tree

    an object of class phylo

    node

    the node to check

    + +

    Value

    + +

    the size of the largest child clade

    + +
    + +
    + + +
    +
    +

    Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

    +
    + +
    +

    Site built with pkgdown 1.6.1.

    +
    + +
    +
    + + + + + + + + diff --git a/docs/reference/get_min_cluster_size.html b/docs/reference/get_min_cluster_size.html new file mode 100644 index 00000000..2f40b233 --- /dev/null +++ b/docs/reference/get_min_cluster_size.html @@ -0,0 +1,215 @@ + + + + + + + + +Tree method for getting the min child clade size of a node — get_min_cluster_size • VISION + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + + +
    + +
    +
    +
    +

    Tree method for getting the min child clade size of a node

    + Source: R/Utilities.R + +
    + +
    +

    Tree method for getting the min child clade size of a node

    +
    + + 
    get_min_cluster_size(tree, node)
    + +

    Arguments

    + + + + + + + + + + +
    tree

    an object of class phylo

    node

    the node to check

    + +

    Value

    + +

    the size of the smallest child clade

    + +
    + +
    + + +
    +
    +

    Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

    +
    + +
    +

    Site built with pkgdown 1.6.1.

    +
    + +
    +
    + + + + + + + + diff --git a/docs/reference/get_parent.html b/docs/reference/get_parent.html new file mode 100644 index 00000000..a3d45b3d --- /dev/null +++ b/docs/reference/get_parent.html @@ -0,0 +1,215 @@ + + + + + + + + +Get the parent of a node — get_parent • VISION + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + + +
    + +
    +
    +
    +

    Get the parent of a node

    + Source: R/Utilities.R + +
    + +
    +

    Get the parent of a node

    +
    + + 
    get_parent(tree, node)
    + +

    Arguments

    + + + + + + + + + + +
    tree

    an object of class phylo

    node

    the node to get parent

    + +

    Value

    + +

    the immediate parent of the mode, or the node if it is root

    + +
    + +
    + + +
    +
    +

    Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

    +
    + +
    +

    Site built with pkgdown 1.6.1.

    +
    + +
    +
    + + + + + + + + diff --git a/docs/reference/group_modules_enrichment.html b/docs/reference/group_modules_enrichment.html new file mode 100644 index 00000000..f899f5e4 --- /dev/null +++ b/docs/reference/group_modules_enrichment.html @@ -0,0 +1,225 @@ + + + + + + + + +Make the clusters for the modules by enrichment. +For now we just assign each signature to each cluster, could filter to only include once, +so that each one appears in the modules x sigs table. — group_modules_enrichment • VISION + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + + +
    + +
    +
    +
    +

    Make the clusters for the modules by enrichment. +For now we just assign each signature to each cluster, could filter to only include once, +so that each one appears in the modules x sigs table.

    + Source: R/methods-Module.R + +
    + +
    +

    Make the clusters for the modules by enrichment. +For now we just assign each signature to each cluster, could filter to only include once, +so that each one appears in the modules x sigs table.

    +
    + + 
    group_modules_enrichment(stats, pvals)
    + +

    Arguments

    + + + + + + + + + + +
    stats

    overlap stats from calc_set_enrichment

    pvals

    overlap p values from calc_set_enrichment

    + +

    Value

    + +

    assignments of each signature to each module

    + +
    + +
    + + +
    +
    +

    Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

    +
    + +
    +

    Site built with pkgdown 1.6.1.

    +
    + +
    +
    + + + + + + + + diff --git a/docs/reference/hsCalculateModuleScores.html b/docs/reference/hsCalculateModuleScores.html new file mode 100644 index 00000000..bdbbf898 --- /dev/null +++ b/docs/reference/hsCalculateModuleScores.html @@ -0,0 +1,229 @@ + + + + + + + + +Create Hotspot Modules and calculate module scores given a HS object +with local correlations already calculated — hsCalculateModuleScores • VISION + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + + +
    + +
    +
    +
    +

    Create Hotspot Modules and calculate module scores given a HS object +with local correlations already calculated

    + Source: R/methods-Module.R + +
    + +
    +

    Create Hotspot Modules and calculate module scores given a HS object +with local correlations already calculated

    +
    + + 
    hsCalculateModuleScores(
+  hs,
+  min_gene_threshold = 20,
+  clustering_fdr = 0.5,
+  plot = F
+)
    + +

    Arguments

    + + + + + + + + + + + + + + +
    hs

    the Hotspot object, must have ran compute_local_correlations already

    min_gene_threshold

    min genes per module

    clustering_fdr

    p value for clustering genes

    + +

    Value

    + +

    the modified hs object

    + +
    + +
    + + +
    +
    +

    Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

    +
    + +
    +

    Site built with pkgdown 1.6.1.

    +
    + +
    +
    + + + + + + + + diff --git a/docs/reference/hsComputeAutoCorrelations.html b/docs/reference/hsComputeAutoCorrelations.html new file mode 100644 index 00000000..76475339 --- /dev/null +++ b/docs/reference/hsComputeAutoCorrelations.html @@ -0,0 +1,223 @@ + + + + + + + + +Compute Hotspot auto correlations — hsComputeAutoCorrelations • VISION + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + + +
    + +
    +
    +
    +

    Compute Hotspot auto correlations

    + Source: R/methods-Module.R + +
    + +
    +

    Compute Hotspot auto correlations

    +
    + + 
    hsComputeAutoCorrelations(
+  hs,
+  number_top_genes = 1000,
+  autocorrelation_fdr = 0.05
+)
    + +

    Arguments

    + + + + + + + + + + + + + + +
    hs

    the Hotspot object

    number_top_genes

    Hotspot argument for number of genes to consider

    autocorrelation_fdr

    threshold for significance for genes autocorr

    + +

    Value

    + +

    list of HS genes

    + +
    + +
    + + +
    +
    +

    Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

    +
    + +
    +

    Site built with pkgdown 1.6.1.

    +
    + +
    +
    + + + + + + + + diff --git a/docs/reference/hsComputeLocalCorrelations.html b/docs/reference/hsComputeLocalCorrelations.html new file mode 100644 index 00000000..a4c1bb55 --- /dev/null +++ b/docs/reference/hsComputeLocalCorrelations.html @@ -0,0 +1,220 @@ + + + + + + + + +Interface function to compute local correlations for Hotspot +Warning: modifies the hs argument — hsComputeLocalCorrelations • VISION + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + + +
    + +
    +
    +
    +

    Interface function to compute local correlations for Hotspot +Warning: modifies the hs argument

    + Source: R/methods-Module.R + +
    + +
    +

    Interface function to compute local correlations for Hotspot +Warning: modifies the hs argument

    +
    + + 
    hsComputeLocalCorrelations(hs, hs_genes)
    + +

    Arguments

    + + + + + + + + + + +
    hs

    the Hotspot object

    hs_genes

    Hotspot genes

    + +

    Value

    + +

    the populated hs object

    + +
    + +
    + + +
    +
    +

    Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

    +
    + +
    +

    Site built with pkgdown 1.6.1.

    +
    + +
    +
    + + + + + + + + diff --git a/docs/reference/hsCreateKnnGraph.html b/docs/reference/hsCreateKnnGraph.html new file mode 100644 index 00000000..b86d1257 --- /dev/null +++ b/docs/reference/hsCreateKnnGraph.html @@ -0,0 +1,203 @@ + + + + + + + + +Init KNN graph in Hotspot object — hsCreateKnnGraph • VISION + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + + +
    + +
    +
    +
    +

    Init KNN graph in Hotspot object

    + Source: R/methods-Module.R + +
    + +
    +

    Init KNN graph in Hotspot object

    +
    + + 
    hsCreateKnnGraph(hs, object, n_neighbors = NULL)
    + + +

    Value

    + +

    the Hotspot object with KNN initialized

    + +
    + +
    + + +
    +
    +

    Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

    +
    + +
    +

    Site built with pkgdown 1.6.1.

    +
    + +
    +
    + + + + + + + + diff --git a/docs/reference/hsInit.html b/docs/reference/hsInit.html new file mode 100644 index 00000000..55fe22d4 --- /dev/null +++ b/docs/reference/hsInit.html @@ -0,0 +1,227 @@ + + + + + + + + +Init Hotspot object from Vision Object — hsInit • VISION + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + + +
    + +
    +
    +
    +

    Init Hotspot object from Vision Object

    + Source: R/methods-Module.R + +
    + +
    +

    Init Hotspot object from Vision Object

    +
    + + 
    hsInit(object, model = "normal", tree = F, num_umi = NULL, logdata = FALSE)
    + +

    Arguments

    + + + + + + + + + + + + + + + + + + + + + + +
    object

    the Vision Object

    model

    the model for Hotspot (ie "normal", "danb"...)

    tree

    boolean, whether to use the tree as ls

    num_umi

    df of barcodes x num_umi

    logdata

    boolean, log the expression data, avoid for danb

    + +

    Value

    + +

    the Hotspot object

    + +
    + +
    + + +
    +
    +

    Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

    +
    + +
    +

    Site built with pkgdown 1.6.1.

    +
    + +
    +
    + + + + + + + + diff --git a/docs/reference/is_tip.html b/docs/reference/is_tip.html new file mode 100644 index 00000000..fa9058fc --- /dev/null +++ b/docs/reference/is_tip.html @@ -0,0 +1,215 @@ + + + + + + + + +Check if a child is a tip — is_tip • VISION + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + + +
    + +
    +
    +
    +

    Check if a child is a tip

    + Source: R/Utilities.R + +
    + +
    +

    Check if a child is a tip

    +
    + + 
    is_tip(tree, node)
    + +

    Arguments

    + + + + + + + + + + +
    tree

    an object of class phylo

    node

    the node to check

    + +

    Value

    + +

    true or false

    + +
    + +
    + + +
    +
    +

    Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

    +
    + +
    +

    Site built with pkgdown 1.6.1.

    +
    + +
    +
    + + + + + + + + diff --git a/docs/reference/knn_tree.html b/docs/reference/knn_tree.html new file mode 100644 index 00000000..7a918929 --- /dev/null +++ b/docs/reference/knn_tree.html @@ -0,0 +1,225 @@ + + + + + + + + +Helper KNN Function for Trees — knn_tree • VISION + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + + +
    + +
    +
    +
    +

    Helper KNN Function for Trees

    + Source: R/Utilities.R + +
    + +
    +

    Computes nearest-neighbor indices and distances +in serial. Query is over all points and results +do not include the self-distance.

    +
    + + 
    knn_tree(leaves, k, distances)
    + +

    Arguments

    + + + + + + + + + + + + + + +
    leaves

    leaves to find the nearest neighbors of

    k

    number of neighbors to query

    distances

    matrix of Samples x Samples matrix of cophenetic tree distances

    + +

    Value

    + +

    list with two items: + index: Samples x K matrix of neighbor indices + dist: Samples x K matrix of neighbor distances

    + +
    + +
    + + +
    +
    +

    Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

    +
    + +
    +

    Site built with pkgdown 1.6.1.

    +
    + +
    +
    + + + + + + + + diff --git a/docs/reference/lcaBasedHotspotNeighbors.html b/docs/reference/lcaBasedHotspotNeighbors.html new file mode 100644 index 00000000..2edbc949 --- /dev/null +++ b/docs/reference/lcaBasedHotspotNeighbors.html @@ -0,0 +1,208 @@ + + + + + + + + +Add custom tree based neighbor and weights to a Hotspot object — lcaBasedHotspotNeighbors • VISION + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + + +
    + +
    +
    +
    +

    Add custom tree based neighbor and weights to a Hotspot object

    + Source: R/methods-Module.R + +
    + +
    +

    @param tree object of class phylo + @param the Hotspot object to add the nw to + @param minSize the minimum number of neighbors of the node + @return the Hotspot object

    +

    @export

    +
    + + 
    lcaBasedHotspotNeighbors(tree, hotspot, minSize = 20)
    + + + +
    + +
    + + +
    +
    +

    Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

    +
    + +
    +

    Site built with pkgdown 1.6.1.

    +
    + +
    +
    + + + + + + + + diff --git a/docs/reference/lcaBasedTreeKNN.html b/docs/reference/lcaBasedTreeKNN.html new file mode 100644 index 00000000..1f11d98d --- /dev/null +++ b/docs/reference/lcaBasedTreeKNN.html @@ -0,0 +1,206 @@ + + + + + + + + +Add custom tree based neighbor and weights to a hotspot object — lcaBasedTreeKNN • VISION + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + + +
    + +
    +
    +
    +

    Add custom tree based neighbor and weights to a hotspot object

    + Source: R/Utilities.R + +
    + +
    +

    @param tree object of class phylo + @param the hotspot object to add the nw to + @param minSize the minimum number of neighbors of the node + @return the hotspot object

    +
    + + 
    lcaBasedTreeKNN(tree, minSize = 20)
    + + + +
    + +
    + + +
    +
    +

    Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

    +
    + +
    +

    Site built with pkgdown 1.6.1.

    +
    + +
    +
    + + + + + + + + diff --git a/docs/reference/lca_based_depth.html b/docs/reference/lca_based_depth.html new file mode 100644 index 00000000..a0986893 --- /dev/null +++ b/docs/reference/lca_based_depth.html @@ -0,0 +1,219 @@ + + + + + + + + +Depth of tip1 parent immediately after LCA(tip1, tip2) — lca_based_depth • VISION + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + + +
    + +
    +
    +
    +

    Depth of tip1 parent immediately after LCA(tip1, tip2)

    + Source: R/Utilities.R + +
    + +
    +

    Depth of tip1 parent immediately after LCA(tip1, tip2)

    +
    + + 
    lca_based_depth(tree, tip1, tip2)
    + +

    Arguments

    + + + + + + + + + + + + + + +
    tree

    an object of class phylo

    tip1

    the first leaf

    tip2

    the second leaf

    + +

    Value

    + +

    the trivial distance between tip1, tip2

    + +
    + +
    + + +
    +
    +

    Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

    +
    + +
    +

    Site built with pkgdown 1.6.1.

    +
    + +
    +
    + + + + + + + + diff --git a/docs/reference/loadHotspotObject.html b/docs/reference/loadHotspotObject.html new file mode 100644 index 00000000..d2c6354e --- /dev/null +++ b/docs/reference/loadHotspotObject.html @@ -0,0 +1,215 @@ + + + + + + + + +Load in an existing Hotspot object from bytes or a file — loadHotspotObject • VISION + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + + +
    + +
    +
    +
    +

    Load in an existing Hotspot object from bytes or a file

    + Source: R/methods-Module.R + +
    + +
    +

    Load in an existing Hotspot object from bytes or a file

    +
    + + 
    loadHotspotObject(file = NULL, bytes = NULL)
    + +

    Arguments

    + + + + + + + + + + +
    file

    optional path to an existing file containing pickled bytes (format 0)

    bytes

    optional R character vector of bytes created by calcHotspotModules

    + +

    Value

    + +

    an externalptr to a Hotspot Object loaded in the R reticulate session

    + +
    + +
    + + +
    +
    +

    Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

    +
    + +
    +

    Site built with pkgdown 1.6.1.

    +
    + +
    +
    + + + + + + + + diff --git a/docs/reference/maxSizeCladewiseTreeCluster.html b/docs/reference/maxSizeCladewiseTreeCluster.html new file mode 100644 index 00000000..bb9e70fa --- /dev/null +++ b/docs/reference/maxSizeCladewiseTreeCluster.html @@ -0,0 +1,221 @@ + + + + + + + + +Performs a breadth first search to create a specific number of clusters +Clusters are split to prioritize max cluster size — maxSizeCladewiseTreeCluster • VISION + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + + +
    + +
    +
    +
    +

    Performs a breadth first search to create a specific number of clusters +Clusters are split to prioritize max cluster size

    + Source: R/Microclusters.R + +
    + +
    +

    Performs a breadth first search to create a specific number of clusters +Clusters are split to prioritize max cluster size

    +
    + + 
    maxSizeCladewiseTreeCluster(tree, target = 10)
    + +

    Arguments

    + + + + + + + + + + +
    tree

    object of class phylo

    target

    number of clusters to attempt to generate

    + +

    Value

    + +

    List of clusters, each entry being a vector of tips representing +samples in the cluster.

    + +
    + +
    + + +
    +
    +

    Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

    +
    + +
    +

    Site built with pkgdown 1.6.1.

    +
    + +
    +
    + + + + + + + + diff --git a/docs/reference/minSizeCladeNeighbors.html b/docs/reference/minSizeCladeNeighbors.html new file mode 100644 index 00000000..fd5eee86 --- /dev/null +++ b/docs/reference/minSizeCladeNeighbors.html @@ -0,0 +1,219 @@ + + + + + + + + +Get's the nearest >= min size neighbors of a node based on clade structure — minSizeCladeNeighbors • VISION + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + + +
    + +
    +
    +
    +

    Get's the nearest >= min size neighbors of a node based on clade structure

    + Source: R/Utilities.R + +
    + +
    +

    Get's the nearest >= min size neighbors of a node based on clade structure

    +
    + + 
    minSizeCladeNeighbors(tree, tip, minSize = 20)
    + +

    Arguments

    + + + + + + + + + + + + + + +
    tree

    an object of class phylo

    tip

    the tip to find the neighbors of

    minSize

    the minimum number of neighbors of the node (excludes self)

    + +

    Value

    + +

    the neighbors

    + +
    + +
    + + +
    +
    +

    Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

    +
    + +
    +

    Site built with pkgdown 1.6.1.

    +
    + +
    +
    + + + + + + + + diff --git a/docs/reference/phyloAnalyze-PhyloVision-method.html b/docs/reference/phyloAnalyze-PhyloVision-method.html new file mode 100644 index 00000000..8478a6dd --- /dev/null +++ b/docs/reference/phyloAnalyze-PhyloVision-method.html @@ -0,0 +1,209 @@ + + + + + + + + +Analyze a PhyloVision object — phyloAnalyze,PhyloVision-method • VISION + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + + +
    + +
    +
    +
    +

    Analyze a PhyloVision object

    + Source: R/methods-Vision.R + +
    + +
    +

    Analyze a PhyloVision object

    +
    + + 
    # S4 method for PhyloVision
+phyloAnalyze(object, hotspot = FALSE)
    + +

    Arguments

    + + + + + + +
    ...

    arguments passed to the base Vision constructor

    + + +
    + +
    + + +
    +
    +

    Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

    +
    + +
    +

    Site built with pkgdown 1.6.1.

    +
    + +
    +
    + + + + + + + + diff --git a/docs/reference/runHotspot.html b/docs/reference/runHotspot.html new file mode 100644 index 00000000..314a2bff --- /dev/null +++ b/docs/reference/runHotspot.html @@ -0,0 +1,268 @@ + + + + + + + + +Perform Hotspot analysis on Vision Object — runHotspot • VISION + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + + +
    + +
    +
    +
    +

    Perform Hotspot analysis on Vision Object

    + Source: R/methods-Module.R + +
    + +
    +

    Perform Hotspot analysis on Vision Object

    +
    + + 
    runHotspot(
+  object,
+  model = "normal",
+  tree = FALSE,
+  number_top_genes = 1000,
+  num_umi = NULL,
+  min_gene_threshold = 20,
+  n_neighbors = NULL,
+  autocorrelation_fdr = 0.05,
+  clustering_fdr = 0.5,
+  logdata = FALSE
+)
    + +

    Arguments

    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    object

    Vision Object

    model

    model argument for Hotspot, one of

      +

    • normal

      • +

    • danb

      • +

    • bernoulli

      • +

    • none

      • +
    tree

    whether to use tree as latent space. If TRUE, object should have +a tree slot.

    number_top_genes

    Hotspot argument for number of genes to consider

    num_umi

    optional dataframe containing umi counts in first column for +barcodes

    min_gene_threshold

    minimum number of genes in Hotspot module

    n_neighbors

    number of neighbors to consider in latent space

    autocorrelation_fdr

    threshold for significance for genes autocorr

    clustering_fdr

    threshold for significance for clustering modules

    logdata

    boolean, log the expression data, avoid for danb +Populates the modData, HotspotModuleScores, ModuleSignatureEnrichment +and HotspotObject slots of object, as well as recalculates signature scores +for new modules.

    + +

    Value

    + +

    the modified Vision object

    + +
    + +
    + + +
    +
    +

    Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

    +
    + +
    +

    Site built with pkgdown 1.6.1.

    +
    + +
    +
    + + + + + + + + diff --git a/docs/reference/saveHSBytestToPickle.html b/docs/reference/saveHSBytestToPickle.html new file mode 100644 index 00000000..be5a7ee9 --- /dev/null +++ b/docs/reference/saveHSBytestToPickle.html @@ -0,0 +1,212 @@ + + + + + + + + +Save bytes in the Hotspot object slot to a file — saveHSBytestToPickle • VISION + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + + +
    + +
    +
    +
    +

    Save bytes in the Hotspot object slot to a file

    + Source: R/methods-Module.R + +
    + +
    +

    Save bytes in the Hotspot object slot to a file

    +
    + + 
    saveHSBytestToPickle(path, bytes)
    + +

    Arguments

    + + + + + + + + + + +
    path

    the file path

    bytes

    the raw bytes, like in the Hotspot slot of a VISION Object

    + + +
    + +
    + + +
    +
    +

    Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

    +
    + +
    +

    Site built with pkgdown 1.6.1.

    +
    + +
    +
    + + + + + + + + diff --git a/docs/reference/treeClusterMinCladeSize.html b/docs/reference/treeClusterMinCladeSize.html new file mode 100644 index 00000000..18085cfc --- /dev/null +++ b/docs/reference/treeClusterMinCladeSize.html @@ -0,0 +1,216 @@ + + + + + + + + +Generate clade-clusters for a tree of minimum size (unless children of root) — treeClusterMinCladeSize • VISION + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + + +
    + +
    +
    +
    +

    Generate clade-clusters for a tree of minimum size (unless children of root)

    + Source: R/Microclusters.R + +
    + +
    +

    Generate clade-clusters for a tree of minimum size (unless children of root)

    +
    + + 
    treeClusterMinCladeSize(tree, minSize = 30)
    + +

    Arguments

    + + + + + + + + + + +
    tree

    object of class phylo

    minSize

    minimum clade size for a clade to be expanded

    + +

    Value

    + +

    List of clusters, each entry being a vector of tips representing +WARNING: This won't work well for tree's with broad multifurcations

    + +
    + +
    + + +
    +
    +

    Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

    +
    + +
    +

    Site built with pkgdown 1.6.1.

    +
    + +
    +
    + + + + + + + + diff --git a/docs/reference/trivial_dist.html b/docs/reference/trivial_dist.html new file mode 100644 index 00000000..25f86a56 --- /dev/null +++ b/docs/reference/trivial_dist.html @@ -0,0 +1,221 @@ + + + + + + + + +Trivial distance function for arbitrary tree clustering — trivial_dist • VISION + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + + +
    + +
    +
    +
    +

    Trivial distance function for arbitrary tree clustering

    + Source: R/Utilities.R + +
    + +
    +

    Number of mutations along path from tip1 to LCA(tip1, tip2) +Ensures if on same clade, join.

    +
    + + 
    trivial_dist(tree, tip1, tip2)
    + +

    Arguments

    + + + + + + + + + + + + + + +
    tree

    an object of class phylo

    tip1

    the first leaf

    tip2

    the second leaf

    + +

    Value

    + +

    the trivial distance between tip1, tip2

    + +
    + +
    + + +
    +
    +

    Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

    +
    + +
    +

    Site built with pkgdown 1.6.1.

    +
    + +
    +
    + + + + + + + + diff --git a/docs/reference/ultrametric_tree.html b/docs/reference/ultrametric_tree.html new file mode 100644 index 00000000..ccc27f05 --- /dev/null +++ b/docs/reference/ultrametric_tree.html @@ -0,0 +1,211 @@ + + + + + + + + +Generate an ultrametric tree — ultrametric_tree • VISION + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + + +
    + +
    +
    +
    +

    Generate an ultrametric tree

    + Source: R/Utilities.R + +
    + +
    +

    Generate an ultrametric tree

    +
    + + 
    ultrametric_tree(tree)
    + +

    Arguments

    + + + + + + +
    tree

    an object of class phylo

    + +

    Value

    + +

    a tree with edge distances such that it is ultrametric.

    + +
    + +
    + + +
    +
    +

    Developed by Matt Jones, David Detomaso, Tal Ashuach, Yanay Rosen.

    +
    + +
    +

    Site built with pkgdown 1.6.1.

    +
    + +
    +
    + + + + + + + + diff --git a/man/PhyloVision-class.Rd b/man/PhyloVision-class.Rd new file mode 100644 index 00000000..40c9a1c8 --- /dev/null +++ b/man/PhyloVision-class.Rd @@ -0,0 +1,19 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/AllGenerics.R, R/methods-Vision.R +\name{PhyloVision} +\alias{PhyloVision} +\alias{PhyloVision,phylo-method} +\title{Initializes a new PhyloVision Object} +\usage{ +PhyloVision(tree, ...) + +\S4method{PhyloVision}{phylo}(tree, ...) +} +\arguments{ +\item{tree}{parsed ape tree} + +\item{...}{arguments passed to the base Vision constructor} +} +\description{ +Initializes a new PhyloVision Object +} diff --git a/man/addHotspotToVision.Rd b/man/addHotspotToVision.Rd new file mode 100644 index 00000000..385ce4b8 --- /dev/null +++ b/man/addHotspotToVision.Rd @@ -0,0 +1,19 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/methods-Module.R +\name{addHotspotToVision} +\alias{addHotspotToVision} +\title{Add HS python obj to vision OBJECT} +\usage{ +addHotspotToVision(object, hs) +} +\arguments{ +\item{object}{Vision object} + +\item{hs}{python hs object} +} +\value{ +Vision object with hs populated +} +\description{ +Add HS python obj to vision OBJECT +} diff --git a/man/analyzeHotspotObjectVision.Rd b/man/analyzeHotspotObjectVision.Rd new file mode 100644 index 00000000..5ff769fa --- /dev/null +++ b/man/analyzeHotspotObjectVision.Rd @@ -0,0 +1,28 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/methods-Module.R +\name{analyzeHotspotObjectVision} +\alias{analyzeHotspotObjectVision} +\title{Analyze a Hotspot object using built in methods such +such as local correlation, signature overlap, etc. +Necessary to run this function for Hotspot functionality in viewer to work.} +\usage{ +analyzeHotspotObjectVision(object, hs, tree = FALSE) +} +\arguments{ +\item{object}{the VISION object} + +\item{hs}{the Hotspot python object loaded by Reticulate} + +\item{tree}{whether to use tree as latent space. If TRUE, object should have a tree} +} +\value{ +the modified VISION object with the following slots filled: +Populates the modData, HotspotModuleScores, ModuleSignatureEnrichment +and HotspotObject slots of object, as well as recalculates signature scores +for new modules. +} +\description{ +Analyze a Hotspot object using built in methods such +such as local correlation, signature overlap, etc. +Necessary to run this function for Hotspot functionality in viewer to work. +} diff --git a/man/analyzeLocalCorrelationsModules.Rd b/man/analyzeLocalCorrelationsModules.Rd new file mode 100644 index 00000000..23c212ff --- /dev/null +++ b/man/analyzeLocalCorrelationsModules.Rd @@ -0,0 +1,22 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/methods-Module.R +\name{analyzeLocalCorrelationsModules} +\alias{analyzeLocalCorrelationsModules} +\title{Compute local correlations for all modules} +\usage{ +analyzeLocalCorrelationsModules(object, tree = FALSE) +} +\arguments{ +\item{object}{the VISION object} + +\item{tree}{whether to use the tree object as latent space for neighbors} +} +\value{ +the VISION object with values set for the analysis results +} +\description{ +This is the main analysis function. For each filtered dataset, a set of +different projection onto low-dimensional space are computed, and the +consistency of the resulting space with the signature scores is computed +to find signals that are captured successfully by the projections. +} diff --git a/man/ancestor_at_depth.Rd b/man/ancestor_at_depth.Rd new file mode 100644 index 00000000..b1e1a925 --- /dev/null +++ b/man/ancestor_at_depth.Rd @@ -0,0 +1,21 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/Utilities.R +\name{ancestor_at_depth} +\alias{ancestor_at_depth} +\title{Find the ancestor of a node above a specific depth} +\usage{ +ancestor_at_depth(tree, node, depth) +} +\arguments{ +\item{tree}{an object of class phylo} + +\item{node}{the index of the node} + +\item{depth}{the depth to search to} +} +\value{ +the index of the ancestor node +} +\description{ +Find the ancestor of a node above a specific depth +} diff --git a/man/calcModuleScores.Rd b/man/calcModuleScores.Rd new file mode 100644 index 00000000..9de3cf13 --- /dev/null +++ b/man/calcModuleScores.Rd @@ -0,0 +1,27 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/methods-Module.R +\name{calcModuleScores} +\alias{calcModuleScores} +\title{Calculate module scores (signature scores but on the modules)} +\usage{ +calcModuleScores(object, mod_norm_method = NULL, mod_gene_importance = TRUE) +} +\arguments{ +\item{object}{the VISION object} + +\item{mod_norm_method}{Method to apply to normalize the expression matrix +before calculating signature scores. Valid options are: +"znorm_columns" (default), "none", "znorm_rows", "znorm_rows_then_columns", +or "rank_norm_columns"} + +\item{mod_gene_importance}{whether or not to rank each gene's contribution to +the overall signature score. Default = TRUE. This is used for inspecting +genes in a signature in the output report} +} +\value{ +the VISION object, with the @ModScores and @ModGeneImportance slots populated +} +\description{ +For each module-cell pair, compute a score that captures the level of +correspondence between the cell and the module. +} diff --git a/man/calc_mod_sig_enrichment.Rd b/man/calc_mod_sig_enrichment.Rd new file mode 100644 index 00000000..a4bd18ad --- /dev/null +++ b/man/calc_mod_sig_enrichment.Rd @@ -0,0 +1,19 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/methods-Module.R +\name{calc_mod_sig_enrichment} +\alias{calc_mod_sig_enrichment} +\title{Computes the hypergeometric overlap test for modules and signatures} +\usage{ +calc_mod_sig_enrichment(object, skip_down = TRUE) +} +\arguments{ +\item{object}{the Vision object.} + +\item{skip_down}{whether to ignore down signatures in overlap} +} +\value{ +list(statistic values, p values, clusters of signatures) +} +\description{ +Computes the hypergeometric overlap test for modules and signatures +} diff --git a/man/calc_set_enrichment.Rd b/man/calc_set_enrichment.Rd new file mode 100644 index 00000000..fd603880 --- /dev/null +++ b/man/calc_set_enrichment.Rd @@ -0,0 +1,25 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/methods-Module.R +\name{calc_set_enrichment} +\alias{calc_set_enrichment} +\title{Calculate the hypergeometric enrichment for two sets from a population +Statisic = log (observed overlap / expected overlap) +P value = 1- hypergeometric(observed overlap -1, max(|set1|, |set2|), |genes| - |set1|, min(|set1|, |set2|))} +\usage{ +calc_set_enrichment(set1, set2, genes) +} +\arguments{ +\item{set1}{the first gene set} + +\item{set2}{the second gene set} + +\item{genes}{the population} +} +\value{ +c(statistic, p value) +} +\description{ +Calculate the hypergeometric enrichment for two sets from a population +Statisic = log (observed overlap / expected overlap) +P value = 1- hypergeometric(observed overlap -1, max(|set1|, |set2|), |genes| - |set1|, min(|set1|, |set2|)) +} diff --git a/man/clusterModScores.Rd b/man/clusterModScores.Rd new file mode 100644 index 00000000..5db252c4 --- /dev/null +++ b/man/clusterModScores.Rd @@ -0,0 +1,19 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/methods-Module.R +\name{clusterModScores} +\alias{clusterModScores} +\title{Compute Ranksums Test, for all factor meta data. One level vs all others} +\usage{ +clusterModScores(object, variables = "All") +} +\arguments{ +\item{object}{the VISION object} + +\item{variables}{which columns of the meta-data to use for comparisons} +} +\value{ +the VISION object with the @ClusterComparisons modules slot populated +} +\description{ +Compute Ranksums Test, for all factor meta data. One level vs all others +} diff --git a/man/computeKNNWeights-phylo-method.Rd b/man/computeKNNWeights-phylo-method.Rd new file mode 100644 index 00000000..4cceaabd --- /dev/null +++ b/man/computeKNNWeights-phylo-method.Rd @@ -0,0 +1,31 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/Projections.R +\name{computeKNNWeights,phylo-method} +\alias{computeKNNWeights,phylo-method} +\title{Compute for each vector the weights to apply to it's K nearest neighbors} +\usage{ +\S4method{computeKNNWeights}{phylo}( + object, + K = round(sqrt(length(object$tip.label))), + lcaKNN = FALSE, + minSize = 20 +) +} +\arguments{ +\item{object}{tree to use for KNN} + +\item{K}{Number of neighbors to consider.} + +\item{lcaKNN}{whether to use LCA based KNN (cluster by minimum size), if false defaults to cophenetic distance (random tie breaking). +WARNING: lcaKNN doesn't perform well with broad multifurcations} +} +\value{ +a list of two items: + indices: matrix, cells X neighbors + Each row specifies indices of nearest neighbors + weights: matrix, cells X neighbors + Corresponding weights to nearest neighbors +} +\description{ +Compute for each vector the weights to apply to it's K nearest neighbors +} diff --git a/man/depthBasedCladewiseTreeCluster.Rd b/man/depthBasedCladewiseTreeCluster.Rd new file mode 100644 index 00000000..ea4c7219 --- /dev/null +++ b/man/depthBasedCladewiseTreeCluster.Rd @@ -0,0 +1,22 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/Microclusters.R +\name{depthBasedCladewiseTreeCluster} +\alias{depthBasedCladewiseTreeCluster} +\title{Performs a breadth first search to create a specific number of clusters. +Clusters are split based on depth.} +\usage{ +depthBasedCladewiseTreeCluster(tree, target = 10) +} +\arguments{ +\item{tree}{object of class phylo} + +\item{target}{number of clusters to attempt to generate} +} +\value{ +List of clusters, each entry being a vector of indices representing +samples in the cluster. +} +\description{ +Performs a breadth first search to create a specific number of clusters. +Clusters are split based on depth. +} diff --git a/man/depthBasedTreeCluster.Rd b/man/depthBasedTreeCluster.Rd new file mode 100644 index 00000000..52f36c00 --- /dev/null +++ b/man/depthBasedTreeCluster.Rd @@ -0,0 +1,22 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/Microclusters.R +\name{depthBasedTreeCluster} +\alias{depthBasedTreeCluster} +\title{Performs a binary search on a depth d such that +if depth(LCA(u, v)) <= d then u and v are in the same cluster} +\usage{ +depthBasedTreeCluster(tree, target = 10) +} +\arguments{ +\item{tree}{object of class phylo} + +\item{target}{number of clusters to attempt to generate} +} +\value{ +List of clusters, each entry being a vector of indices representing +samples in the cluster. +} +\description{ +Performs a binary search on a depth d such that +if depth(LCA(u, v)) <= d then u and v are in the same cluster +} diff --git a/man/draw_hotspot_heatmap.Rd b/man/draw_hotspot_heatmap.Rd new file mode 100644 index 00000000..77c59f4d --- /dev/null +++ b/man/draw_hotspot_heatmap.Rd @@ -0,0 +1,16 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/methods-Module.R +\name{draw_hotspot_heatmap} +\alias{draw_hotspot_heatmap} +\title{Draw Modules Heatmap (Gene x Gene)} +\usage{ +draw_hotspot_heatmap(hs, palette = paletteer_d("ggsci::default_nejm")) +} +\arguments{ +\item{hs}{the Hotspot Object} + +\item{palette}{palette} +} +\description{ +Draw Modules Heatmap (Gene x Gene) +} diff --git a/man/find_knn_parallel_tree.Rd b/man/find_knn_parallel_tree.Rd new file mode 100644 index 00000000..06464e4e --- /dev/null +++ b/man/find_knn_parallel_tree.Rd @@ -0,0 +1,23 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/Utilities.R +\name{find_knn_parallel_tree} +\alias{find_knn_parallel_tree} +\title{Parallel KNN for Trees} +\usage{ +find_knn_parallel_tree(tree, K) +} +\arguments{ +\item{tree}{an object of class phylo} + +\item{K}{number of neighbors to query} +} +\value{ +list with two items: + index: Samples x K matrix of neighbor indices + dist: Samples x K matrix of neighbor distances +} +\description{ +Computes nearest-neighbor indices and distances +in parallel. Query is over all points and results +do not include the self-distance. +} diff --git a/man/find_root.Rd b/man/find_root.Rd new file mode 100644 index 00000000..04e789d9 --- /dev/null +++ b/man/find_root.Rd @@ -0,0 +1,17 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/Utilities.R +\name{find_root} +\alias{find_root} +\title{Find the root node} +\usage{ +find_root(tree) +} +\arguments{ +\item{tree}{an object of class phylo} +} +\value{ +the index of the root node +} +\description{ +Find the root node +} diff --git a/man/generateOverlapSignatures.Rd b/man/generateOverlapSignatures.Rd new file mode 100644 index 00000000..89006ca2 --- /dev/null +++ b/man/generateOverlapSignatures.Rd @@ -0,0 +1,17 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/methods-Module.R +\name{generateOverlapSignatures} +\alias{generateOverlapSignatures} +\title{Generates signature objects for the overlap sets between modules and signatures} +\usage{ +generateOverlapSignatures(object) +} +\arguments{ +\item{object}{the Vision object} +} +\value{ +Vision Object, populates the modData slot with overlap signatures. +} +\description{ +Generates signature objects for the overlap sets between modules and signatures +} diff --git a/man/get_all_children.Rd b/man/get_all_children.Rd new file mode 100644 index 00000000..725982c0 --- /dev/null +++ b/man/get_all_children.Rd @@ -0,0 +1,19 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/Utilities.R +\name{get_all_children} +\alias{get_all_children} +\title{Get all the tip children of a node.} +\usage{ +get_all_children(tree, node) +} +\arguments{ +\item{tree}{an object of class phylo} + +\item{node}{the node to check} +} +\value{ +the tips +} +\description{ +Get all the tip children of a node. +} diff --git a/man/get_children.Rd b/man/get_children.Rd new file mode 100644 index 00000000..3485612a --- /dev/null +++ b/man/get_children.Rd @@ -0,0 +1,19 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/Utilities.R +\name{get_children} +\alias{get_children} +\title{Find the children of a node} +\usage{ +get_children(tree, node) +} +\arguments{ +\item{tree}{an object of class phylo} + +\item{node}{the node to get the children of} +} +\value{ +the children +} +\description{ +Find the children of a node +} diff --git a/man/get_max_cluster_size.Rd b/man/get_max_cluster_size.Rd new file mode 100644 index 00000000..66e44fe3 --- /dev/null +++ b/man/get_max_cluster_size.Rd @@ -0,0 +1,19 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/Utilities.R +\name{get_max_cluster_size} +\alias{get_max_cluster_size} +\title{Tree method for getting the max child clade size of a node} +\usage{ +get_max_cluster_size(tree, node) +} +\arguments{ +\item{tree}{an object of class phylo} + +\item{node}{the node to check} +} +\value{ +the size of the largest child clade +} +\description{ +Tree method for getting the max child clade size of a node +} diff --git a/man/get_min_cluster_size.Rd b/man/get_min_cluster_size.Rd new file mode 100644 index 00000000..a8d04c25 --- /dev/null +++ b/man/get_min_cluster_size.Rd @@ -0,0 +1,19 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/Utilities.R +\name{get_min_cluster_size} +\alias{get_min_cluster_size} +\title{Tree method for getting the min child clade size of a node} +\usage{ +get_min_cluster_size(tree, node) +} +\arguments{ +\item{tree}{an object of class phylo} + +\item{node}{the node to check} +} +\value{ +the size of the smallest child clade +} +\description{ +Tree method for getting the min child clade size of a node +} diff --git a/man/get_parent.Rd b/man/get_parent.Rd new file mode 100644 index 00000000..f644f6bf --- /dev/null +++ b/man/get_parent.Rd @@ -0,0 +1,19 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/Utilities.R +\name{get_parent} +\alias{get_parent} +\title{Get the parent of a node} +\usage{ +get_parent(tree, node) +} +\arguments{ +\item{tree}{an object of class phylo} + +\item{node}{the node to get parent} +} +\value{ +the immediate parent of the mode, or the node if it is root +} +\description{ +Get the parent of a node +} diff --git a/man/group_modules_enrichment.Rd b/man/group_modules_enrichment.Rd new file mode 100644 index 00000000..cbad6036 --- /dev/null +++ b/man/group_modules_enrichment.Rd @@ -0,0 +1,23 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/methods-Module.R +\name{group_modules_enrichment} +\alias{group_modules_enrichment} +\title{Make the clusters for the modules by enrichment. +For now we just assign each signature to each cluster, could filter to only include once, +so that each one appears in the modules x sigs table.} +\usage{ +group_modules_enrichment(stats, pvals) +} +\arguments{ +\item{stats}{overlap stats from calc_set_enrichment} + +\item{pvals}{overlap p values from calc_set_enrichment} +} +\value{ +assignments of each signature to each module +} +\description{ +Make the clusters for the modules by enrichment. +For now we just assign each signature to each cluster, could filter to only include once, +so that each one appears in the modules x sigs table. +} diff --git a/man/hsCalculateModuleScores.Rd b/man/hsCalculateModuleScores.Rd new file mode 100644 index 00000000..6a53874f --- /dev/null +++ b/man/hsCalculateModuleScores.Rd @@ -0,0 +1,28 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/methods-Module.R +\name{hsCalculateModuleScores} +\alias{hsCalculateModuleScores} +\title{Create Hotspot Modules and calculate module scores given a HS object +with local correlations already calculated} +\usage{ +hsCalculateModuleScores( + hs, + min_gene_threshold = 20, + clustering_fdr = 0.5, + plot = F +) +} +\arguments{ +\item{hs}{the Hotspot object, must have ran compute_local_correlations already} + +\item{min_gene_threshold}{min genes per module} + +\item{clustering_fdr}{p value for clustering genes} +} +\value{ +the modified hs object +} +\description{ +Create Hotspot Modules and calculate module scores given a HS object +with local correlations already calculated +} diff --git a/man/hsComputeAutoCorrelations.Rd b/man/hsComputeAutoCorrelations.Rd new file mode 100644 index 00000000..9f278e9f --- /dev/null +++ b/man/hsComputeAutoCorrelations.Rd @@ -0,0 +1,25 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/methods-Module.R +\name{hsComputeAutoCorrelations} +\alias{hsComputeAutoCorrelations} +\title{Compute Hotspot auto correlations} +\usage{ +hsComputeAutoCorrelations( + hs, + number_top_genes = 1000, + autocorrelation_fdr = 0.05 +) +} +\arguments{ +\item{hs}{the Hotspot object} + +\item{number_top_genes}{Hotspot argument for number of genes to consider} + +\item{autocorrelation_fdr}{threshold for significance for genes autocorr} +} +\value{ +list of HS genes +} +\description{ +Compute Hotspot auto correlations +} diff --git a/man/hsComputeLocalCorrelations.Rd b/man/hsComputeLocalCorrelations.Rd new file mode 100644 index 00000000..94a9f86d --- /dev/null +++ b/man/hsComputeLocalCorrelations.Rd @@ -0,0 +1,21 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/methods-Module.R +\name{hsComputeLocalCorrelations} +\alias{hsComputeLocalCorrelations} +\title{Interface function to compute local correlations for Hotspot +Warning: modifies the hs argument} +\usage{ +hsComputeLocalCorrelations(hs, hs_genes) +} +\arguments{ +\item{hs}{the Hotspot object} + +\item{hs_genes}{Hotspot genes} +} +\value{ +the populated hs object +} +\description{ +Interface function to compute local correlations for Hotspot +Warning: modifies the hs argument +} diff --git a/man/hsCreateKnnGraph.Rd b/man/hsCreateKnnGraph.Rd new file mode 100644 index 00000000..487fa60f --- /dev/null +++ b/man/hsCreateKnnGraph.Rd @@ -0,0 +1,14 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/methods-Module.R +\name{hsCreateKnnGraph} +\alias{hsCreateKnnGraph} +\title{Init KNN graph in Hotspot object} +\usage{ +hsCreateKnnGraph(hs, object, n_neighbors = NULL) +} +\value{ +the Hotspot object with KNN initialized +} +\description{ +Init KNN graph in Hotspot object +} diff --git a/man/hsInit.Rd b/man/hsInit.Rd new file mode 100644 index 00000000..62684dfa --- /dev/null +++ b/man/hsInit.Rd @@ -0,0 +1,25 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/methods-Module.R +\name{hsInit} +\alias{hsInit} +\title{Init Hotspot object from Vision Object} +\usage{ +hsInit(object, model = "normal", tree = F, num_umi = NULL, logdata = FALSE) +} +\arguments{ +\item{object}{the Vision Object} + +\item{model}{the model for Hotspot (ie "normal", "danb"...)} + +\item{tree}{boolean, whether to use the tree as ls} + +\item{num_umi}{df of barcodes x num_umi} + +\item{logdata}{boolean, log the expression data, avoid for danb} +} +\value{ +the Hotspot object +} +\description{ +Init Hotspot object from Vision Object +} diff --git a/man/is_tip.Rd b/man/is_tip.Rd new file mode 100644 index 00000000..392519aa --- /dev/null +++ b/man/is_tip.Rd @@ -0,0 +1,19 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/Utilities.R +\name{is_tip} +\alias{is_tip} +\title{Check if a child is a tip} +\usage{ +is_tip(tree, node) +} +\arguments{ +\item{tree}{an object of class phylo} + +\item{node}{the node to check} +} +\value{ +true or false +} +\description{ +Check if a child is a tip +} diff --git a/man/knn_tree.Rd b/man/knn_tree.Rd new file mode 100644 index 00000000..06a07fab --- /dev/null +++ b/man/knn_tree.Rd @@ -0,0 +1,25 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/Utilities.R +\name{knn_tree} +\alias{knn_tree} +\title{Helper KNN Function for Trees} +\usage{ +knn_tree(leaves, k, distances) +} +\arguments{ +\item{leaves}{leaves to find the nearest neighbors of} + +\item{k}{number of neighbors to query} + +\item{distances}{matrix of Samples x Samples matrix of cophenetic tree distances} +} +\value{ +list with two items: + index: Samples x K matrix of neighbor indices + dist: Samples x K matrix of neighbor distances +} +\description{ +Computes nearest-neighbor indices and distances +in serial. Query is over all points and results +do not include the self-distance. +} diff --git a/man/lcaBasedHotspotNeighbors.Rd b/man/lcaBasedHotspotNeighbors.Rd new file mode 100644 index 00000000..f0bda411 --- /dev/null +++ b/man/lcaBasedHotspotNeighbors.Rd @@ -0,0 +1,16 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/methods-Module.R +\name{lcaBasedHotspotNeighbors} +\alias{lcaBasedHotspotNeighbors} +\title{Add custom tree based neighbor and weights to a Hotspot object} +\usage{ +lcaBasedHotspotNeighbors(tree, hotspot, minSize = 20) +} +\description{ +@param tree object of class phylo + @param the Hotspot object to add the nw to + @param minSize the minimum number of neighbors of the node + @return the Hotspot object + + @export +} diff --git a/man/lcaBasedTreeKNN.Rd b/man/lcaBasedTreeKNN.Rd new file mode 100644 index 00000000..d23767f8 --- /dev/null +++ b/man/lcaBasedTreeKNN.Rd @@ -0,0 +1,14 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/Utilities.R +\name{lcaBasedTreeKNN} +\alias{lcaBasedTreeKNN} +\title{Add custom tree based neighbor and weights to a hotspot object} +\usage{ +lcaBasedTreeKNN(tree, minSize = 20) +} +\description{ +@param tree object of class phylo + @param the hotspot object to add the nw to + @param minSize the minimum number of neighbors of the node + @return the hotspot object +} diff --git a/man/lca_based_depth.Rd b/man/lca_based_depth.Rd new file mode 100644 index 00000000..a99042e2 --- /dev/null +++ b/man/lca_based_depth.Rd @@ -0,0 +1,21 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/Utilities.R +\name{lca_based_depth} +\alias{lca_based_depth} +\title{Depth of tip1 parent immediately after LCA(tip1, tip2)} +\usage{ +lca_based_depth(tree, tip1, tip2) +} +\arguments{ +\item{tree}{an object of class phylo} + +\item{tip1}{the first leaf} + +\item{tip2}{the second leaf} +} +\value{ +the trivial distance between tip1, tip2 +} +\description{ +Depth of tip1 parent immediately after LCA(tip1, tip2) +} diff --git a/man/loadHotspotObject.Rd b/man/loadHotspotObject.Rd new file mode 100644 index 00000000..31449911 --- /dev/null +++ b/man/loadHotspotObject.Rd @@ -0,0 +1,19 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/methods-Module.R +\name{loadHotspotObject} +\alias{loadHotspotObject} +\title{Load in an existing Hotspot object from bytes or a file} +\usage{ +loadHotspotObject(file = NULL, bytes = NULL) +} +\arguments{ +\item{file}{optional path to an existing file containing pickled bytes (format 0)} + +\item{bytes}{optional R character vector of bytes created by calcHotspotModules} +} +\value{ +an externalptr to a Hotspot Object loaded in the R reticulate session +} +\description{ +Load in an existing Hotspot object from bytes or a file +} diff --git a/man/maxSizeCladewiseTreeCluster.Rd b/man/maxSizeCladewiseTreeCluster.Rd new file mode 100644 index 00000000..4d51b2fa --- /dev/null +++ b/man/maxSizeCladewiseTreeCluster.Rd @@ -0,0 +1,22 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/Microclusters.R +\name{maxSizeCladewiseTreeCluster} +\alias{maxSizeCladewiseTreeCluster} +\title{Performs a breadth first search to create a specific number of clusters +Clusters are split to prioritize max cluster size} +\usage{ +maxSizeCladewiseTreeCluster(tree, target = 10) +} +\arguments{ +\item{tree}{object of class phylo} + +\item{target}{number of clusters to attempt to generate} +} +\value{ +List of clusters, each entry being a vector of tips representing +samples in the cluster. +} +\description{ +Performs a breadth first search to create a specific number of clusters +Clusters are split to prioritize max cluster size +} diff --git a/man/minSizeCladeNeighbors.Rd b/man/minSizeCladeNeighbors.Rd new file mode 100644 index 00000000..2765184b --- /dev/null +++ b/man/minSizeCladeNeighbors.Rd @@ -0,0 +1,21 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/Utilities.R +\name{minSizeCladeNeighbors} +\alias{minSizeCladeNeighbors} +\title{Get's the nearest >= min size neighbors of a node based on clade structure} +\usage{ +minSizeCladeNeighbors(tree, tip, minSize = 20) +} +\arguments{ +\item{tree}{an object of class phylo} + +\item{tip}{the tip to find the neighbors of} + +\item{minSize}{the minimum number of neighbors of the node (excludes self)} +} +\value{ +the neighbors +} +\description{ +Get's the nearest >= min size neighbors of a node based on clade structure +} diff --git a/man/phyloAnalyze-PhyloVision-method.Rd b/man/phyloAnalyze-PhyloVision-method.Rd new file mode 100644 index 00000000..09448af3 --- /dev/null +++ b/man/phyloAnalyze-PhyloVision-method.Rd @@ -0,0 +1,15 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/methods-Vision.R +\name{phyloAnalyze,PhyloVision-method} +\alias{phyloAnalyze,PhyloVision-method} +\alias{phyloAnalyze} +\title{Analyze a PhyloVision object} +\usage{ +\S4method{phyloAnalyze}{PhyloVision}(object, hotspot = FALSE) +} +\arguments{ +\item{...}{arguments passed to the base Vision constructor} +} +\description{ +Analyze a PhyloVision object +} diff --git a/man/runHotspot.Rd b/man/runHotspot.Rd new file mode 100644 index 00000000..2f61795f --- /dev/null +++ b/man/runHotspot.Rd @@ -0,0 +1,56 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/methods-Module.R +\name{runHotspot} +\alias{runHotspot} +\title{Perform Hotspot analysis on Vision Object} +\usage{ +runHotspot( + object, + model = "normal", + tree = FALSE, + number_top_genes = 1000, + num_umi = NULL, + min_gene_threshold = 20, + n_neighbors = NULL, + autocorrelation_fdr = 0.05, + clustering_fdr = 0.5, + logdata = FALSE +) +} +\arguments{ +\item{object}{Vision Object} + +\item{model}{model argument for Hotspot, one of \itemize{ +\item normal +\item danb +\item bernoulli +\item none +}} + +\item{tree}{whether to use tree as latent space. If TRUE, object should have +a tree slot.} + +\item{number_top_genes}{Hotspot argument for number of genes to consider} + +\item{num_umi}{optional dataframe containing umi counts in first column for +barcodes} + +\item{min_gene_threshold}{minimum number of genes in Hotspot module} + +\item{n_neighbors}{number of neighbors to consider in latent space} + +\item{autocorrelation_fdr}{threshold for significance for genes autocorr} + +\item{clustering_fdr}{threshold for significance for clustering modules} + +\item{logdata}{boolean, log the expression data, avoid for danb +Populates the modData, HotspotModuleScores, ModuleSignatureEnrichment +and HotspotObject slots of object, as well as recalculates signature scores +for new modules.} +} +\value{ +the modified Vision object +} +\description{ +Perform Hotspot analysis on Vision Object +} diff --git a/man/saveHSBytestToPickle.Rd b/man/saveHSBytestToPickle.Rd new file mode 100644 index 00000000..e41aa0f1 --- /dev/null +++ b/man/saveHSBytestToPickle.Rd @@ -0,0 +1,16 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/methods-Module.R +\name{saveHSBytestToPickle} +\alias{saveHSBytestToPickle} +\title{Save bytes in the Hotspot object slot to a file} +\usage{ +saveHSBytestToPickle(path, bytes) +} +\arguments{ +\item{path}{the file path} + +\item{bytes}{the raw bytes, like in the Hotspot slot of a VISION Object} +} +\description{ +Save bytes in the Hotspot object slot to a file +} diff --git a/man/treeClusterMinCladeSize.Rd b/man/treeClusterMinCladeSize.Rd new file mode 100644 index 00000000..ec928ea1 --- /dev/null +++ b/man/treeClusterMinCladeSize.Rd @@ -0,0 +1,20 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/Microclusters.R +\name{treeClusterMinCladeSize} +\alias{treeClusterMinCladeSize} +\title{Generate clade-clusters for a tree of minimum size (unless children of root)} +\usage{ +treeClusterMinCladeSize(tree, minSize = 30) +} +\arguments{ +\item{tree}{object of class phylo} + +\item{minSize}{minimum clade size for a clade to be expanded} +} +\value{ +List of clusters, each entry being a vector of tips representing +WARNING: This won't work well for tree's with broad multifurcations +} +\description{ +Generate clade-clusters for a tree of minimum size (unless children of root) +} diff --git a/man/trivial_dist.Rd b/man/trivial_dist.Rd new file mode 100644 index 00000000..a4a05b74 --- /dev/null +++ b/man/trivial_dist.Rd @@ -0,0 +1,22 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/Utilities.R +\name{trivial_dist} +\alias{trivial_dist} +\title{Trivial distance function for arbitrary tree clustering} +\usage{ +trivial_dist(tree, tip1, tip2) +} +\arguments{ +\item{tree}{an object of class phylo} + +\item{tip1}{the first leaf} + +\item{tip2}{the second leaf} +} +\value{ +the trivial distance between tip1, tip2 +} +\description{ +Number of mutations along path from tip1 to LCA(tip1, tip2) +Ensures if on same clade, join. +} diff --git a/man/ultrametric_tree.Rd b/man/ultrametric_tree.Rd new file mode 100644 index 00000000..09a5bbb1 --- /dev/null +++ b/man/ultrametric_tree.Rd @@ -0,0 +1,17 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/Utilities.R +\name{ultrametric_tree} +\alias{ultrametric_tree} +\title{Generate an ultrametric tree} +\usage{ +ultrametric_tree(tree) +} +\arguments{ +\item{tree}{an object of class phylo} +} +\value{ +a tree with edge distances such that it is ultrametric. +} +\description{ +Generate an ultrametric tree +} From 91214dc48213cd8711c77496393af9b97110b59c Mon Sep 17 00:00:00 2001 From: Yanay1 Date: Thu, 19 Aug 2021 11:22:46 -0700 Subject: [PATCH 54/62] release changes --- R/Utilities.R | 5 ++--- R/methods-Module.R | 5 +---- docs/articles/phyloVision.html | 30 +++++++++++++++-------------- docs/articles/spatialHotspot.html | 12 +++++++----- docs/articles/trajectories.html | 2 +- docs/pkgdown.yml | 2 +- docs/reference/lcaBasedTreeKNN.html | 12 +++++------- hotspot_env.yaml | 30 ----------------------------- man/lcaBasedTreeKNN.Rd | 5 ++--- vignettes/phyloVision.Rmd | 8 +++++++- vignettes/spatialHotspot.Rmd | 6 ++++++ 11 files changed, 48 insertions(+), 69 deletions(-) delete mode 100644 hotspot_env.yaml diff --git a/R/Utilities.R b/R/Utilities.R index c7eb65cf..9c40b5dd 100644 --- a/R/Utilities.R +++ b/R/Utilities.R @@ -853,11 +853,10 @@ find_knn_parallel_tree <- function(tree, K) { -#' Add custom tree based neighbor and weights to a hotspot object +#' Generate neighbors and weights for a tree object, based on LCA. #' #' @param tree object of class phylo -#' @param the hotspot object to add the nw to -#' @param minSize the minimum number of neighbors of the node +#' @param minSize the minimum number of neighbors per node #' @return the hotspot object lcaBasedTreeKNN <- function(tree, minSize=20) { tips <- tree$tip.label diff --git a/R/methods-Module.R b/R/methods-Module.R index e870adb1..34cf6ffe 100644 --- a/R/methods-Module.R +++ b/R/methods-Module.R @@ -748,10 +748,7 @@ draw_hotspot_heatmap <- function(hs, palette = paletteer_d("ggsci::default_nejm" example_genes[[mod]] = sample(hs$modules[hs$modules == mod], 5) } } - print(module_to_col) - print(col_mapping[order(names(col_mapping))]) - print(col_mapping) - print(example_genes) + modules = data.frame("module" = hs$modules) modules$module = as.character(modules$module) ha = rowAnnotation(df = modules, diff --git a/docs/articles/phyloVision.html b/docs/articles/phyloVision.html index 3eaf50b4..7afe642b 100644 --- a/docs/articles/phyloVision.html +++ b/docs/articles/phyloVision.html @@ -132,6 +132,8 @@

    require(devtools) install_github("YosefLab/VISION")

    Once VISION and R are installed, you may load in VISION using library(VISION).

    +

    Hotspot is a tool for identifying informative genes (and gene modules) in a single-cell dataset. Hotspot is installed directly from the git repository using the following command:

    +
    pip install git+https://github.com/yoseflab/Hotspot.git

    @@ -144,7 +146,7 @@

  • Browsing results

    • First, we need to load VISION, reticulate and ape.

    -
    +
     knitr::opts_chunk$set(echo = TRUE)
 library(VISION)
 library(reticulate)
@@ -153,7 +155,7 @@ 
    
 
    
 Creating a PhyloVision Object with a Tree
    
 
    Vision objects now support dendrograms for visualization and analysis. To create the PhyloVision object, you need all of the same data, an expression matrix, and metadata and/or signatures, but you also include a tree object from the Ape package.
    
-
    +
     # Read the expression and meta data
 file_path <- "data/embryogenesis" # Replace the path
 
@@ -190,17 +192,17 @@ 
    
 
    
 Running PhyloVision analysis
    
 
    Next, we can perform the normal Vision analysis using the tree as the latent space.
    
-
    +
     vis <- phyloAnalyze(vis)
    
 
    
-
    
+
    
 
    
-Running Hotpost analysis
    
+Running Hotspot analysis

    We can also perform Hotspot module analysis. The expression data is already logged for us.

    -
    +
     vis <- runHotspot(vis, model="normal", tree=TRUE, min_gene_threshold=50, n_neighbors = 30, number_top_genes = nrow(expr), logdata=FALSE)
    
 
    The full Hotspot API is exposed for analysis as well. For more on the Hotspot API see here
    
-
    +
     # Init Hotspot
 hs <- hsInit(vis, model = "normal", tree=TRUE, logdata=FALSE)
 # Init Hotspot KNN
@@ -214,16 +216,16 @@ 
    
 # Cluster Hotspot modules and perform Vision based analysis on HS Modules and 
 vis <- analyzeHotspotObjectVision(vis, hs, tree=TRUE)
    
 
    We can also access further Hotspot functionality using Reticulate and Python.
    
-
    +
     hs <- loadHotspotObject(bytes=vis@Hotspot)
 library(reticulate)
 use_python('/usr/bin/python3')
    
-
    import matplotlib.pyplot as plt
-import hotspot
-hs.plot_local_correlations()
-plt.show()
    
+
    import matplotlib.pyplot as plt
+import hotspot
+hs.plot_local_correlations()
+plt.show()
    
 
    Note: the heatmap can also be visualized like so:
    
-
    +
@@ -232,7 +234,7 @@ 
    
 
    
 Viewing Results
    
 
    Finally, we can launch the Vision browser.
    
-
    +
 
    
 
    
diff --git a/docs/articles/spatialHotspot.html b/docs/articles/spatialHotspot.html
index 3f265304..0ddce6f1 100644
--- a/docs/articles/spatialHotspot.html
+++ b/docs/articles/spatialHotspot.html
@@ -132,6 +132,8 @@ 
    
 require(devtools)
 install_github("YosefLab/VISION")
    
 
    Once VISION and R are installed, you may load in VISION using library(VISION).
    
+
    Hotspot is a tool for identifying informative genes (and gene modules) in a single-cell dataset. Hotspot is installed directly from the git repository using the following command:
    
+
    pip install git+https://github.com/yoseflab/Hotspot.git
    
 
    
 
    
 
    
@@ -144,7 +146,7 @@ 
    
 
  • Browsing results
    • 
 
 
    First, we need to load VISION and reticulate.
    
-
    +
     knitr::opts_chunk$set(echo = TRUE)
 library(VISION)
 library(reticulate)
    
@@ -152,7 +154,7 @@ 
    
 
    
 Creating a Vision Object
    
 
    First, we create a Vision object
    
-
    +
     # Read the expression and meta data
 file_path <- "data/spatial" # Replace the path
 
@@ -186,14 +188,14 @@ 
    
 
    
 Running an analysis
    
 
    Next, we can perform the normal Vision analysis using the spatial coordinates as the latent space.
    
-
    +
     vis <- analyze(vis)
    
 
    
 
    
 
    
 Running Hotpsot analysis
    
 
    We can also perform Hotspot module analysis. For more on the Hotspot API see here and the PhyloVision vignette.
    
-
    +
     vis@params$latentSpace$projectionGenes <- rownames(vis@exprData) # Use all genes.
 vis <- runHotspot(vis, model="bernoulli", num_umi=meta["num_umi"], logdata=FALSE)
    
 
    
@@ -201,7 +203,7 @@ 
    
 
    
 Viewing results
    
 
    Finally, we can launch the Vision browser.
    
-
    +
 
    
 
    
diff --git a/docs/articles/trajectories.html b/docs/articles/trajectories.html
index 6a019dca..d7960c10 100644
--- a/docs/articles/trajectories.html
+++ b/docs/articles/trajectories.html
@@ -206,7 +206,7 @@ 
    
 sessionInfo()
    
 
    ## R version 4.0.4 (2021-02-15)
 ## Platform: x86_64-apple-darwin19.6.0 (64-bit)
-## Running under: macOS Catalina 10.15.7
+## Running under: macOS Big Sur 10.16
 ## 
 ## Matrix products: default
 ## BLAS:   /usr/local/Cellar/openblas/0.3.13/lib/libopenblasp-r0.3.13.dylib
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
index 06f1087d..1e4d1ffd 100644
--- a/docs/pkgdown.yml
+++ b/docs/pkgdown.yml
@@ -11,7 +11,7 @@ articles:
   web_only/10xData: 10xData.html
   web_only/Seurat: Seurat.html
   web_only/SignatureAutocorrelation: SignatureAutocorrelation.html
-last_built: 2021-06-17T17:55Z
+last_built: 2021-08-19T18:21Z
 urls:
   reference: https://yoseflab.github.io/VISION//reference
   article: https://yoseflab.github.io/VISION//articles
diff --git a/docs/reference/lcaBasedTreeKNN.html b/docs/reference/lcaBasedTreeKNN.html
index 1f11d98d..21fda540 100644
--- a/docs/reference/lcaBasedTreeKNN.html
+++ b/docs/reference/lcaBasedTreeKNN.html
@@ -6,7 +6,7 @@
 
 
 
-Add custom tree based neighbor and weights to a hotspot object — lcaBasedTreeKNN • VISION
+Generate neighbors and weights for a tree object, based on LCA. — lcaBasedTreeKNN • VISION
 
 
 
@@ -48,10 +48,9 @@
   
   
 
-
+
 
 
 
@@ -160,15 +159,14 @@
 
    
   
    
     
    
-    
    Add custom tree based neighbor and weights to a hotspot object
    
+    
    Generate neighbors and weights for a tree object, based on LCA.
    
     Source: R/Utilities.R
     
     
    
 
     
    
     
    @param tree object of class phylo
- @param the hotspot object to add the nw to
- @param minSize the minimum number of neighbors of the node
+ @param minSize the minimum number of neighbors per node
  @return the hotspot object
    
     
    
 
diff --git a/hotspot_env.yaml b/hotspot_env.yaml
deleted file mode 100644
index 1e00da19..00000000
--- a/hotspot_env.yaml
+++ /dev/null
@@ -1,30 +0,0 @@
-name: vision_hotspot
-channels:
-  - defaults
-dependencies:
-  - pip=20.1.1
-  - python=3.8.3
-  - pip:
-    - cycler==0.10.0
-    - git+https://github.com/yoseflab/Hotspot.git
-    - joblib==0.15.1
-    - kiwisolver==1.2.0
-    - llvmlite==0.33.0
-    - matplotlib==3.2.2
-    - numba==0.50.1
-    - numpy==1.19.0
-    - pandas==1.0.5
-    - patsy==0.5.1
-    - pyparsing==2.4.7
-    - python-dateutil==2.8.1
-    - pytz==2020.1
-    - scikit-learn==0.23.1
-    - scipy==1.5.0
-    - seaborn==0.10.1
-    - six==1.15.0
-    - statsmodels==0.11.1
-    - threadpoolctl==2.1.0
-    - tqdm==4.46.1
-    - ete3
-prefix: /Users/yanay/Desktop/VISION/envs
-
diff --git a/man/lcaBasedTreeKNN.Rd b/man/lcaBasedTreeKNN.Rd
index d23767f8..5c50646d 100644
--- a/man/lcaBasedTreeKNN.Rd
+++ b/man/lcaBasedTreeKNN.Rd
@@ -2,13 +2,12 @@
 % Please edit documentation in R/Utilities.R
 \name{lcaBasedTreeKNN}
 \alias{lcaBasedTreeKNN}
-\title{Add custom tree based neighbor and weights to a hotspot object}
+\title{Generate neighbors and weights for a tree object, based on LCA.}
 \usage{
 lcaBasedTreeKNN(tree, minSize = 20)
 }
 \description{
 @param tree object of class phylo
- @param the hotspot object to add the nw to
- @param minSize the minimum number of neighbors of the node
+ @param minSize the minimum number of neighbors per node
  @return the hotspot object
 }
diff --git a/vignettes/phyloVision.Rmd b/vignettes/phyloVision.Rmd
index 8e92eb91..09124c1a 100644
--- a/vignettes/phyloVision.Rmd
+++ b/vignettes/phyloVision.Rmd
@@ -19,6 +19,12 @@ install_github("YosefLab/VISION")
 
 Once VISION and R are installed, you may load in VISION using `library(VISION)`.
 
+Hotspot is a tool for identifying informative genes (and gene modules) in a single-cell dataset. Hotspot is installed directly from the git repository using the following command:
+
+```
+pip install git+https://github.com/yoseflab/Hotspot.git
+```
+
 # Using PhyloVision
 
 Running an analysis with vision consists of three steps:
@@ -93,7 +99,7 @@ Next, we can perform the normal Vision analysis using the tree as the latent spa
 ``` {r analyze, eval=F}
 vis <- phyloAnalyze(vis)
 ```
-## Running Hotpost analysis
+## Running Hotspot analysis
 
 We can also perform Hotspot module analysis. The expression data is already logged for us.
 ```{r hotspot, eval=F}
diff --git a/vignettes/spatialHotspot.Rmd b/vignettes/spatialHotspot.Rmd
index 2c422a55..5f75ec4b 100644
--- a/vignettes/spatialHotspot.Rmd
+++ b/vignettes/spatialHotspot.Rmd
@@ -18,6 +18,12 @@ install_github("YosefLab/VISION")
 
 Once VISION and R are installed, you may load in VISION using `library(VISION)`.
 
+Hotspot is a tool for identifying informative genes (and gene modules) in a single-cell dataset. Hotspot is installed directly from the git repository using the following command:
+
+```
+pip install git+https://github.com/yoseflab/Hotspot.git
+```
+
 # Using VISION
 
 Running an analysis with vision consists of three steps:

From a4a5ceefc6c6d9aafffcbdbd25e74e8eefb7c486 Mon Sep 17 00:00:00 2001
From: Yanay1 
Date: Thu, 19 Aug 2021 11:41:15 -0700
Subject: [PATCH 55/62] modified subset tree

---
 R/methods-Vision.R              | 5 ++++-
 docs/articles/phyloVision.html  | 2 +-
 docs/articles/trajectories.html | 1 +
 docs/pkgdown.yml                | 2 +-
 vignettes/phyloVision.Rmd       | 2 +-
 vignettes/trajectories.Rmd      | 2 ++
 6 files changed, 10 insertions(+), 4 deletions(-)

diff --git a/R/methods-Vision.R b/R/methods-Vision.R
index a097c27c..5d95d54e 100644
--- a/R/methods-Vision.R
+++ b/R/methods-Vision.R
@@ -119,7 +119,10 @@ setMethod("Vision", signature(data = "matrixORSparse"),
             }
 
             if (!is.null(tree)) {
-                data = data[,tree$tip.label]
+                # Subset matrix
+                data <- data[,tree$tip.label]
+                # Subset Tree
+                tree <- keep.tip(tree, colnames(data)) 
             }
 
             .Object@exprData <- data
diff --git a/docs/articles/phyloVision.html b/docs/articles/phyloVision.html
index 7afe642b..a439f24a 100644
--- a/docs/articles/phyloVision.html
+++ b/docs/articles/phyloVision.html
@@ -175,7 +175,7 @@ 
    
 # Construct the Vision object
 vis <- PhyloVision(tree=tree, data=expr, signatures=sig, meta=meta, num_neighbors=30, projection_genes= rownames(expr))
    
 
    Tree
    
-
    The ape phylogeny object. Singleton edges should be collapsed prior to use. The tree should be filtered to have the same cell (leaf) names as the expression data.
    
+
    The ape phylogeny object. Singleton edges should be collapsed prior to use. Ensure that leaf names correspond to same names used in the expression matrix.
    
 
    Expression Data
    
 
    The provided expression data should be scaled and normalized. It is recommended to apply more advanced normalization procedures such as batch correction or removal of technical confounders.
    
 
    The expression data should not be log-transformed prior to loading into VISION.
    
diff --git a/docs/articles/trajectories.html b/docs/articles/trajectories.html
index d7960c10..188fc598 100644
--- a/docs/articles/trajectories.html
+++ b/docs/articles/trajectories.html
@@ -127,6 +127,7 @@ 
    Incorporating a Trajectory Model
    
 
    
 
    
 Introduction
    
+
    Note: this feature is deprecated in VISION 3.0+.
    
 
    To compute Signature consistency scores, VISION needs a cell-cell similarity metric in order to build the neighborhood graph. By default, VISION runs PCA and uses euclidean distances in the reduced space for this purpose. However, if the cells’ variation is better modeled by a trajectory (either linear or tree-like), then distances along the trajectory structure can be used instead.
    
 
    Many tools exist to perform trajectory inference in single cells. The Dynverse project has developed wrappers for 59 recently-published methods and VISION is able to accept the wrapped output of these methods as an input trajectory model.
    
 
    Within the Dynverse trajectory object, VISION depends on two components:
    
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
index 1e4d1ffd..595060d8 100644
--- a/docs/pkgdown.yml
+++ b/docs/pkgdown.yml
@@ -11,7 +11,7 @@ articles:
   web_only/10xData: 10xData.html
   web_only/Seurat: Seurat.html
   web_only/SignatureAutocorrelation: SignatureAutocorrelation.html
-last_built: 2021-08-19T18:21Z
+last_built: 2021-08-19T18:40Z
 urls:
   reference: https://yoseflab.github.io/VISION//reference
   article: https://yoseflab.github.io/VISION//articles
diff --git a/vignettes/phyloVision.Rmd b/vignettes/phyloVision.Rmd
index 09124c1a..81e26998 100644
--- a/vignettes/phyloVision.Rmd
+++ b/vignettes/phyloVision.Rmd
@@ -68,7 +68,7 @@ vis <- PhyloVision(tree=tree, data=expr, signatures=sig, meta=meta, num_neighbor
 ```
 **Tree**
 
-The `ape` phylogeny object. Singleton edges should be collapsed prior to use. The tree should be filtered to have the same cell (leaf) names as the expression data.
+The `ape` phylogeny object. Singleton edges should be collapsed prior to use. Ensure that leaf names correspond to same names used in the expression matrix. 
 
 **Expression Data**
 
diff --git a/vignettes/trajectories.Rmd b/vignettes/trajectories.Rmd
index fda827f0..bfb39ada 100644
--- a/vignettes/trajectories.Rmd
+++ b/vignettes/trajectories.Rmd
@@ -23,6 +23,8 @@ set.seed(6473) ## for reproducibility
 
 # Introduction
 
+*Note: this feature is deprecated in VISION 3.0+.*
+
 To compute Signature consistency scores, VISION needs a cell-cell similarity metric in order to
 build the neighborhood graph.  By default, VISION runs PCA and uses euclidean distances in the reduced
 space for this purpose.  However, if the cells' variation is better modeled by a trajectory (either

From b5e747de4e21201abc094751eef866372da3f8a0 Mon Sep 17 00:00:00 2001
From: Matthew Jones 
Date: Thu, 26 Aug 2021 13:39:07 -0700
Subject: [PATCH 56/62] updated phylovision rmd

---
 DESCRIPTION               |  1 +
 NAMESPACE                 |  1 +
 vignettes/phyloVision.Rmd | 47 ++++++++++++++++++++++++---------------
 3 files changed, 31 insertions(+), 18 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index c5369611..88026868 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -11,6 +11,7 @@ Maintainer: Matt Jones 
 Description: VISION provides functional interpretation of single cell RNA-seq (scRNA-seq) latent manifolds through the use of biological signatures (which can be downloaded from online databases). VISION can operate downstream of other common analyses such as dimensionality reduction, clustering, or trajectory analysis of scRNA-seq data. VISION produces an interactive web-based output report that can be easily shared with other collaborators or the greater scientific community.
 Depends: R (>= 3.4)
 Imports:
+	dplyr,
 	fastICA,
 	igraph,
     irlba,
diff --git a/NAMESPACE b/NAMESPACE
index 0f3f698f..29b0a2c0 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -62,6 +62,7 @@ exportMethods(viewResults)
 import(Matrix)
 import(Rcpp)
 import(ape)
+import(dplyr)
 import(loe)
 import(logging)
 import(methods)
diff --git a/vignettes/phyloVision.Rmd b/vignettes/phyloVision.Rmd
index 81e26998..9b302ad3 100644
--- a/vignettes/phyloVision.Rmd
+++ b/vignettes/phyloVision.Rmd
@@ -8,6 +8,11 @@ vignette: >
   %\VignetteEncoding{UTF-8}
 ---
 
+# Introduction
+As of version 3.0.0, VISION now supports the analysis of scRNA-seq data with respect to a user-defined cell lineage, or phylogeny. In this case, VISION uses the relationships between cells as specified by the phylogeny, as opposed to some user-defined latent space, to conduct the autocorrelation analysis. In this vignette, we demonstrate how a user might use this variant of the VISION pipeline - which we term `PhyloVision` - to analyze a recently published dataset that simultaneously profiled the single-cell transcriptomes and lineages of mouse embryogenesis (Chan et al, Nature 2019).
+
+This tutorial begins by showing users how to create a `PhyloVision` object and performing analysis on it. Then, we demonstrate how this object can be passed into a Hotspot module that will identify de-novo transcriptional gene sets that are autocorrelated on the tree (this is described more below and in the Spatial Hotspot vignette). Finally, we show users how to launch a report for viewing.
+
 # Preliminaries
 
 If you have yet to install VISION, we recommend installing the package from Github to install this package. Full source code can be found at the VISION Github repository, available [here](http://www.github.com/YosefLab/VISION).
@@ -19,20 +24,14 @@ install_github("YosefLab/VISION")
 
 Once VISION and R are installed, you may load in VISION using `library(VISION)`.
 
-Hotspot is a tool for identifying informative genes (and gene modules) in a single-cell dataset. Hotspot is installed directly from the git repository using the following command:
+To enable the Hotspot analysis below, install it directly from the git repository using the following command:
 
 ```
 pip install git+https://github.com/yoseflab/Hotspot.git
 ```
+If you are having trouble installing Hotspot, please refer to the documentation website [here](https://yoseflab.github.io/Hotspot/).
 
-# Using PhyloVision
-
-Running an analysis with vision consists of three steps:
-
-1. Creating the PhyloVision object
-2. Running the `phyloAnalyze` function
-3. Running Hotspot
-4. Browsing results
+# Running PhyloVision
 
 First, we need to load VISION, reticulate and ape.
 ```{r setup, eval=F}
@@ -59,9 +58,14 @@ sig <- paste("data", "h.all.v5.2.symbols.gmt", sep="/")
 
 # Read the tree
 tree <- read.tree(paste(file_path, "embryo_tree.newick", sep="/"))
-# Collapse one mutations
+
+# subset tree and expression matrix
+keep.bcs = intersect(tree$tip.label, colnames(expr))
+tree <- keep.tip(tree, keep.bcs)
+expr <- expr[, keep.bcs]
+
+# Collapse one mutations with ape
 tree <- collapse.singles(tree)
-expr <- expr[, tree$tip.label]
 
 # Construct the Vision object
 vis <- PhyloVision(tree=tree, data=expr, signatures=sig, meta=meta, num_neighbors=30, projection_genes= rownames(expr))
@@ -72,9 +76,7 @@ The `ape` phylogeny object. Singleton edges should be collapsed prior to use. En
 
 **Expression Data**
 
-The provided expression data should be scaled and normalized. It is recommended to apply more advanced normalization procedures such as batch correction or removal of technical confounders.
-
-The expression data should not be log-transformed prior to loading into VISION.
+The provided expression data should be library-normalized. The expression data should not be log-transformed prior to loading into VISION. For more information on the input to VISION, please refer to the central [VISION vignette](VISION_vignette.html)
 
 **Signatures**
 
@@ -101,12 +103,17 @@ vis <- phyloAnalyze(vis)
 ```
 ## Running Hotspot analysis
 
-We can also perform Hotspot module analysis. The expression data is already logged for us.
+As mentioned above, PhyloVision can take advantage of the new Hotspot functionality in VISION. Briefly, Hotspot is a tool for inferring modules of genes that are significantly autocorrelated with one another and a particular latent space (e.g., the first 30 principal components of a gene expression matrix). When combined with PhyloVision, the Hotspot functionality will use the user-defined phylogeny as the latent space.
+
+We can invoke the Hotspot analysis with the function `runHotspot` and setting `tree=True`. Upon doing so, this will identify modules of genes and add these as Signatures to the VISION object for autocorrelation evaluation. Moreover, to add interpretability to this analysis, VISION will also compute the enrichment between all the user-defined Signatures and each Hotspot module. This information will be accessible on the web-based report by selecting the "Hotspot" mode in the top-right of the web-page.
+
+The full Hotspot API is exposed for analysis as well. For more on the Hotspot API see [here](https://yoseflab.github.io/Hotspot/index.html). To note, while it is typically not recommended to use `model="normal"` and `logdata=FALSE` in Hotpsot, we elect to do so because the data here has been previously log-normalized. In more typical single-cell anlayses where the user is working with a library-normalized count matrix, we suggest setting `model="danb"` and `logdata=TRUE`.
+
 ```{r hotspot, eval=F}
 vis <- runHotspot(vis, model="normal", tree=TRUE, min_gene_threshold=50, n_neighbors = 30, number_top_genes = nrow(expr), logdata=FALSE)
 ```
 
-The full Hotspot API is exposed for analysis as well. For more on the Hotspot API see [here](https://yoseflab.github.io/Hotspot/index.html)
+We have additionally exposed the full Hotspot pipeline should a user want to iterate with different parameters:
 ```{r full_h, eval=FALSE}
 # Init Hotspot
 hs <- hsInit(vis, model = "normal", tree=TRUE, logdata=FALSE)
@@ -143,9 +150,13 @@ draw_hotspot_heatmap(hs)
 
 ## Viewing Results
 
-Finally, we can launch the Vision browser.
+Finally, we can launch the Vision browser. If you are local, the following will work:
 ```{r eval=FALSE}
 viewResults(vis)
 ```
 
-
+Else, if you would like to launch from a server, you can use the following settings:
+```{r, eval=FALSE}
+viewResults(vis, host='0.0.0.0', port=8100, browser=F)
+```
+Now, the report will be visible from port `8100` from your server (e.g., http://server-name:8100/Results.html)

From a32e89b9adaf3459b14d772d7f59887aff757114 Mon Sep 17 00:00:00 2001
From: Matthew Jones 
Date: Fri, 27 Aug 2021 15:03:18 -0700
Subject: [PATCH 57/62] updated Hotspot spatial vignette

---
 vignettes/spatialHotspot.Rmd | 32 ++++++++++++++++++--------------
 1 file changed, 18 insertions(+), 14 deletions(-)

diff --git a/vignettes/spatialHotspot.Rmd b/vignettes/spatialHotspot.Rmd
index 5f75ec4b..2a271bc8 100644
--- a/vignettes/spatialHotspot.Rmd
+++ b/vignettes/spatialHotspot.Rmd
@@ -7,18 +7,24 @@ vignette: >
   %\VignetteEngine{knitr::rmarkdown}
   %\VignetteEncoding{UTF-8}
 ---
+
+# Introduction
+In this vignette, we demonstrate how to use VISION to identify de-novo transcriptional gene modules and interpret them. To this end, we use Hotspot - an algorithm that identifies modules of genes that are significantly autocorrelated with one another on some latent space that can be used to define cell-cell similarity (e.g., the first 30 principal components). Qualitatively, this can be interpreted as a co-expression analysis that takes into account the distribution of gene expression values and nuanced cell-cell similarities. If you are more interested in learning more about the algorithm, you can read the [original publication](https://www.cell.com/cell-systems/fulltext/S2405-4712(21)00114-9).
+
+In the example below, we use spatial transcriptomic data from the Slide-seq technology for the Hotspot analysis, following the original [Hotspot tutorial](https://yoseflab.github.io/Hotspot/Spatial_Tutorial.html). Though this analysis is extensible to more typical latent spaces, this is an interesting example where we show that VISION can use spatial coordinates to define cell-cell similarities.
+
 # Preliminaries
 
 If you have yet to install VISION, we recommend installing the package from Github to install this package. Full source code can be found at the VISION Github repository, available [here](http://www.github.com/YosefLab/VISION).
 
-```r
+```r{eval=FALSE}
 require(devtools)
 install_github("YosefLab/VISION")
 ```
 
-Once VISION and R are installed, you may load in VISION using `library(VISION)`.
+Once VISION and R are installed, you may load in VISION using `library(VISION)`. Also make sure that you have installed `reticular` appropriately, as this will be necessary for running Hotspot.
 
-Hotspot is a tool for identifying informative genes (and gene modules) in a single-cell dataset. Hotspot is installed directly from the git repository using the following command:
+You'll also need to install Hotspot, which can be installed directly from the git repository using the following command:
 
 ```
 pip install git+https://github.com/yoseflab/Hotspot.git
@@ -26,18 +32,13 @@ pip install git+https://github.com/yoseflab/Hotspot.git
 
 # Using VISION
 
-Running an analysis with vision consists of three steps:
-
-1. Creating the VISION object
-2. Running the `analyze` function
-3. Running Hotspot
-3. Browsing results
+Below, we first run the VISION pipeline as usual. In addition to importing VISION, we'll have to import `reticulate` for the Hotspot analaysis.
 
 First, we need to load VISION and reticulate.
 ```{r setup, eval=F}
 knitr::opts_chunk$set(echo = TRUE)
 library(VISION)
-library(reticulate)
+library(reticulate) # for the Hotspot analysis
 ```
 
 ## Creating a Vision Object
@@ -64,9 +65,9 @@ vis <- Vision(expr, signatures=c(sig), latentSpace = pos, meta=meta) # TODO add
 ```
 **Expression Data**
 
-The provided expression data should be scaled and normalized. It is recommended to apply more advanced normalization procedures such as batch correction or removal of technical confounders.
+The provided expression data should be library-normalized.
 
-The expression data should not be log-transformed prior to loading into VISION.
+The expression data should not be log-transformed prior to loading into VISION. For more information about how to transform the expression data, refer to the central [VISION vignette](VISION-vignette.html).
 
 **Signatures**
 
@@ -94,15 +95,18 @@ vis <- analyze(vis)
 
 ## Running Hotpsot analysis
 
-We can also perform Hotspot module analysis. For more on the Hotspot API see [here](https://yoseflab.github.io/Hotspot/index.html) and [the PhyloVision vignette](phyloVision.html).
+Conveniently, the Hotspot analysis can be performed directly ontop of the VISION object we just processed. To do so, we'll use the `runHotspot` function which invokes the Hotspot pipeline. For more information about the analysis pipeline & Hotspot API, you can refer the documentation website [here](https://yoseflab.github.io/Hotspot/index.html) and [the PhyloVision vignette](phyloVision.html).
 ```{r hotspot, eval=F}
 vis@params$latentSpace$projectionGenes <- rownames(vis@exprData) # Use all genes.
 vis <- runHotspot(vis, model="bernoulli", num_umi=meta["num_umi"], logdata=FALSE)
 ```
 
+The [PhyloVision vignette](phyloVision.html) additionally describes the additional API that is exposed for iterating on the Hotspot analysis.
+
+After running the Hotpsot module, the VISION object will have populated slots storing the gene modules, the scores for each cell with respect to these new gene modules, and the enrichment score between user-specified signatures and the new Hotspot gene modules. These results can be explored in the Hotspot mode of the VISION web-based report.
 
 ## Viewing results
-Finally, we can launch the Vision browser.
+Finally, we can launch the Vision browser. The results from the Hotspot analysis can be viewed by clicking on the "Hotspot" button on the top-right of the web report.
 ```{r view, eval=F}
 viewResults(vis)
 ```

From cf8f72fd5f8e12a34fd3e529dd2f8e24fe7cdc0d Mon Sep 17 00:00:00 2001
From: Matthew Jones 
Date: Fri, 27 Aug 2021 15:04:16 -0700
Subject: [PATCH 58/62] updated Hotspot spatial vignette

---
 vignettes/spatialHotspot.Rmd | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/vignettes/spatialHotspot.Rmd b/vignettes/spatialHotspot.Rmd
index 2a271bc8..f659b00f 100644
--- a/vignettes/spatialHotspot.Rmd
+++ b/vignettes/spatialHotspot.Rmd
@@ -9,7 +9,7 @@ vignette: >
 ---
 
 # Introduction
-In this vignette, we demonstrate how to use VISION to identify de-novo transcriptional gene modules and interpret them. To this end, we use Hotspot - an algorithm that identifies modules of genes that are significantly autocorrelated with one another on some latent space that can be used to define cell-cell similarity (e.g., the first 30 principal components). Qualitatively, this can be interpreted as a co-expression analysis that takes into account the distribution of gene expression values and nuanced cell-cell similarities. If you are more interested in learning more about the algorithm, you can read the [original publication](https://www.cell.com/cell-systems/fulltext/S2405-4712(21)00114-9).
+In this vignette, we demonstrate how to use the Hotspot module in VISION to identify de-novo transcriptional gene modules and interpret them. To this end, we use Hotspot - an algorithm that identifies modules of genes that are significantly autocorrelated with one another on some latent space that can be used to define cell-cell similarity (e.g., the first 30 principal components). Qualitatively, this can be interpreted as a co-expression analysis that takes into account the distribution of gene expression values and nuanced cell-cell similarities. If you are more interested in learning more about the algorithm, you can read the [original publication](https://www.cell.com/cell-systems/fulltext/S2405-4712(21)00114-9).
 
 In the example below, we use spatial transcriptomic data from the Slide-seq technology for the Hotspot analysis, following the original [Hotspot tutorial](https://yoseflab.github.io/Hotspot/Spatial_Tutorial.html). Though this analysis is extensible to more typical latent spaces, this is an interesting example where we show that VISION can use spatial coordinates to define cell-cell similarities.
 

From b98d61038fb66afeb180d495c9ddaaee7dbabf5b Mon Sep 17 00:00:00 2001
From: Matt Jones 
Date: Fri, 27 Aug 2021 15:12:06 -0700
Subject: [PATCH 59/62] updated spatial hotspot vignette

---
 vignettes/phyloVision.Rmd    | 4 ++--
 vignettes/spatialHotspot.Rmd | 2 ++
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/vignettes/phyloVision.Rmd b/vignettes/phyloVision.Rmd
index 9b302ad3..c83c0fef 100644
--- a/vignettes/phyloVision.Rmd
+++ b/vignettes/phyloVision.Rmd
@@ -17,7 +17,7 @@ This tutorial begins by showing users how to create a `PhyloVision` object and p
 
 If you have yet to install VISION, we recommend installing the package from Github to install this package. Full source code can be found at the VISION Github repository, available [here](http://www.github.com/YosefLab/VISION).
 
-```r
+```r{eval=FALSE}
 require(devtools)
 install_github("YosefLab/VISION")
 ```
@@ -76,7 +76,7 @@ The `ape` phylogeny object. Singleton edges should be collapsed prior to use. En
 
 **Expression Data**
 
-The provided expression data should be library-normalized. The expression data should not be log-transformed prior to loading into VISION. For more information on the input to VISION, please refer to the central [VISION vignette](VISION_vignette.html)
+The provided expression data should be library-normalized. The expression data should not be log-transformed prior to loading into VISION. For more information on the input to VISION, please refer to the central [VISION vignette](VISION_vignette.html).
 
 **Signatures**
 
diff --git a/vignettes/spatialHotspot.Rmd b/vignettes/spatialHotspot.Rmd
index f659b00f..d1231911 100644
--- a/vignettes/spatialHotspot.Rmd
+++ b/vignettes/spatialHotspot.Rmd
@@ -96,6 +96,8 @@ vis <- analyze(vis)
 ## Running Hotpsot analysis
 
 Conveniently, the Hotspot analysis can be performed directly ontop of the VISION object we just processed. To do so, we'll use the `runHotspot` function which invokes the Hotspot pipeline. For more information about the analysis pipeline & Hotspot API, you can refer the documentation website [here](https://yoseflab.github.io/Hotspot/index.html) and [the PhyloVision vignette](phyloVision.html).
+
+As described in the original Hotspot vignette, we use the `bernoulli` model because of the low capture rate of the spatial technology. In a typical anlaysis, we would use the `danb` model. 
 ```{r hotspot, eval=F}
 vis@params$latentSpace$projectionGenes <- rownames(vis@exprData) # Use all genes.
 vis <- runHotspot(vis, model="bernoulli", num_umi=meta["num_umi"], logdata=FALSE)

From 420cad1e08002b5ad395b4d3f2bbb72ed6dfeedd Mon Sep 17 00:00:00 2001
From: Matt Jones 
Date: Mon, 30 Aug 2021 14:28:02 -0700
Subject: [PATCH 60/62] added small changes suggested

---
 vignettes/phyloVision.Rmd    |  7 +------
 vignettes/spatialHotspot.Rmd | 10 +++++-----
 2 files changed, 6 insertions(+), 11 deletions(-)

diff --git a/vignettes/phyloVision.Rmd b/vignettes/phyloVision.Rmd
index c83c0fef..5aa0a3f2 100644
--- a/vignettes/phyloVision.Rmd
+++ b/vignettes/phyloVision.Rmd
@@ -11,7 +11,7 @@ vignette: >
 # Introduction
 As of version 3.0.0, VISION now supports the analysis of scRNA-seq data with respect to a user-defined cell lineage, or phylogeny. In this case, VISION uses the relationships between cells as specified by the phylogeny, as opposed to some user-defined latent space, to conduct the autocorrelation analysis. In this vignette, we demonstrate how a user might use this variant of the VISION pipeline - which we term `PhyloVision` - to analyze a recently published dataset that simultaneously profiled the single-cell transcriptomes and lineages of mouse embryogenesis (Chan et al, Nature 2019).
 
-This tutorial begins by showing users how to create a `PhyloVision` object and performing analysis on it. Then, we demonstrate how this object can be passed into a Hotspot module that will identify de-novo transcriptional gene sets that are autocorrelated on the tree (this is described more below and in the Spatial Hotspot vignette). Finally, we show users how to launch a report for viewing.
+This tutorial begins by showing users how to create a `PhyloVision` object and performing analysis on it. Then, we demonstrate how this object can be passed into the Hotspot pipeline that will identify de-novo transcriptional gene sets that are autocorrelated on the tree (this is described more below and in the [Spatial Hotspot vignette](spatialHotspot.html). Finally, we show users how to launch a report for viewing.
 
 # Preliminaries
 
@@ -59,11 +59,6 @@ sig <- paste("data", "h.all.v5.2.symbols.gmt", sep="/")
 # Read the tree
 tree <- read.tree(paste(file_path, "embryo_tree.newick", sep="/"))
 
-# subset tree and expression matrix
-keep.bcs = intersect(tree$tip.label, colnames(expr))
-tree <- keep.tip(tree, keep.bcs)
-expr <- expr[, keep.bcs]
-
 # Collapse one mutations with ape
 tree <- collapse.singles(tree)
 
diff --git a/vignettes/spatialHotspot.Rmd b/vignettes/spatialHotspot.Rmd
index d1231911..381a71d9 100644
--- a/vignettes/spatialHotspot.Rmd
+++ b/vignettes/spatialHotspot.Rmd
@@ -9,7 +9,7 @@ vignette: >
 ---
 
 # Introduction
-In this vignette, we demonstrate how to use the Hotspot module in VISION to identify de-novo transcriptional gene modules and interpret them. To this end, we use Hotspot - an algorithm that identifies modules of genes that are significantly autocorrelated with one another on some latent space that can be used to define cell-cell similarity (e.g., the first 30 principal components). Qualitatively, this can be interpreted as a co-expression analysis that takes into account the distribution of gene expression values and nuanced cell-cell similarities. If you are more interested in learning more about the algorithm, you can read the [original publication](https://www.cell.com/cell-systems/fulltext/S2405-4712(21)00114-9).
+In this vignette, we demonstrate how to use the Hotspot pipeline in VISION to identify de-novo transcriptional gene modules and interpret them. To this end, we use Hotspot - an algorithm that identifies modules of genes that are significantly autocorrelated with one another on some latent space that can be used to define cell-cell similarity (e.g., the first 30 principal components). Qualitatively, this can be interpreted as a co-expression analysis that takes into account the distribution of gene expression values and nuanced cell-cell similarities. If you are interested in learning more about the algorithm, you can read the [original publication](https://www.cell.com/cell-systems/fulltext/S2405-4712(21)00114-9).
 
 In the example below, we use spatial transcriptomic data from the Slide-seq technology for the Hotspot analysis, following the original [Hotspot tutorial](https://yoseflab.github.io/Hotspot/Spatial_Tutorial.html). Though this analysis is extensible to more typical latent spaces, this is an interesting example where we show that VISION can use spatial coordinates to define cell-cell similarities.
 
@@ -22,7 +22,7 @@ require(devtools)
 install_github("YosefLab/VISION")
 ```
 
-Once VISION and R are installed, you may load in VISION using `library(VISION)`. Also make sure that you have installed `reticular` appropriately, as this will be necessary for running Hotspot.
+Once VISION and R are installed, you may load in VISION using `library(VISION)`. Also make sure that you have installed `reticulate` appropriately, as this will be necessary for running Hotspot.
 
 You'll also need to install Hotspot, which can be installed directly from the git repository using the following command:
 
@@ -95,7 +95,7 @@ vis <- analyze(vis)
 
 ## Running Hotpsot analysis
 
-Conveniently, the Hotspot analysis can be performed directly ontop of the VISION object we just processed. To do so, we'll use the `runHotspot` function which invokes the Hotspot pipeline. For more information about the analysis pipeline & Hotspot API, you can refer the documentation website [here](https://yoseflab.github.io/Hotspot/index.html) and [the PhyloVision vignette](phyloVision.html).
+Conveniently, the Hotspot analysis can be performed directly on the VISION object we just processed. To do so, we'll use the `runHotspot` function which invokes the Hotspot pipeline. For more information about the analysis pipeline & Hotspot API, you can refer the documentation website [here](https://yoseflab.github.io/Hotspot/index.html) and [the PhyloVision vignette](phyloVision.html).
 
 As described in the original Hotspot vignette, we use the `bernoulli` model because of the low capture rate of the spatial technology. In a typical anlaysis, we would use the `danb` model. 
 ```{r hotspot, eval=F}
@@ -103,9 +103,9 @@ vis@params$latentSpace$projectionGenes <- rownames(vis@exprData) # Use all genes
 vis <- runHotspot(vis, model="bernoulli", num_umi=meta["num_umi"], logdata=FALSE)
 ```
 
-The [PhyloVision vignette](phyloVision.html) additionally describes the additional API that is exposed for iterating on the Hotspot analysis.
+The [PhyloVision vignette](phyloVision.html) describes the additional API that is exposed for iterating on the Hotspot analysis.
 
-After running the Hotpsot module, the VISION object will have populated slots storing the gene modules, the scores for each cell with respect to these new gene modules, and the enrichment score between user-specified signatures and the new Hotspot gene modules. These results can be explored in the Hotspot mode of the VISION web-based report.
+After running the Hotpsot pipeline, the VISION object will have populated slots storing the gene modules, the scores for each cell with respect to these new gene modules, and the enrichment score between user-specified signatures and the new Hotspot gene modules. These results can be explored in the Hotspot mode of the VISION web-based report.
 
 ## Viewing results
 Finally, we can launch the Vision browser. The results from the Hotspot analysis can be viewed by clicking on the "Hotspot" button on the top-right of the web report.

From fad8d8df514b4dd1bdd7a9d7ce8bd8b87bc45ffb Mon Sep 17 00:00:00 2001
From: Yanay1 
Date: Mon, 30 Aug 2021 14:45:33 -0700
Subject: [PATCH 61/62] updating docs

---
 NAMESPACE                             |  1 -
 docs/articles/VISION-vignette.html    | 13 ++++----
 docs/articles/phyloVision.html        | 44 +++++++++++++++------------
 docs/articles/spatialHotspot.html     | 36 +++++++++++-----------
 docs/pkgdown.yml                      |  2 +-
 docs/reference/matrix_wilcox_cpp.html |  2 +-
 man/matrix_wilcox_cpp.Rd              |  2 +-
 7 files changed, 52 insertions(+), 48 deletions(-)

diff --git a/NAMESPACE b/NAMESPACE
index 29b0a2c0..0f3f698f 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -62,7 +62,6 @@ exportMethods(viewResults)
 import(Matrix)
 import(Rcpp)
 import(ape)
-import(dplyr)
 import(loe)
 import(logging)
 import(methods)
diff --git a/docs/articles/VISION-vignette.html b/docs/articles/VISION-vignette.html
index ff5473a5..5c18e746 100644
--- a/docs/articles/VISION-vignette.html
+++ b/docs/articles/VISION-vignette.html
@@ -186,6 +186,7 @@ 
    
 
    To run an analysis, simply call the analyze function:
    
 
     # Set the number of threads when running parallel computations
+# On Windows, this must either be omitted or set to 1
 options(mc.cores = 2)
 
 vis <- analyze(vis)
    
@@ -200,19 +201,17 @@ 
    
 
    Other options (port, host, browser) can be provided to control how this occurs. For example, if you are launching a report on a remote server (such as an AWS instance) and want to make it accessible to others, run this with host="0.0.0.0", some selected port number (e.g. port=8888), and browser=FALSE (so a browser isn’t auto-opened). Then the report should be available at “<your instance IP address>:8888”. (Note: You will also likely need to enable inbound traffic on your selected port for this to work correctly).
    
 
    Alternately, you can work with the VISION object directly in R. For example:
    
 
    -# Display autocorrelation coefficients for signatures
-head(vis@SigConsistencyScores@sigProjMatrix)
+# Display autocorrelation coefficients, p-values for signatures
+head(getSignatureAutocorrelation(vis))
 
-# View autocorrelation empirical p-values
-head(vis@SigConsistencyScores@emp_pMatrix)
 
 # Plot signature scores for a signature of interest
-tsne <- vis@Projections$tSNE30
-sigScores <- vis@sigScores[, "HALLMARK_INTERFERON_GAMMA_RESPONSE"]
+tsne <- getProjections(vis)[["tSNE30"]]
+sigScores <- getSignatureScores(vis)[, "HALLMARK_INTERFERON_GAMMA_RESPONSE"]
 
 library(ggplot2)
 ggplot() + aes(x=tsne[, 1], y=tsne[, 2], color=sigScores) + geom_point()
    
-
    For more details on the structure of the VISION object see XXX.
    
+
    For more details on accessing computed data within the VISION object, see the References page.
    
 
    
 
    
 
    
diff --git a/docs/articles/phyloVision.html b/docs/articles/phyloVision.html
index a439f24a..4dd1fc47 100644
--- a/docs/articles/phyloVision.html
+++ b/docs/articles/phyloVision.html
@@ -124,27 +124,26 @@ 
    Introduction to PhyloVision and Hotspot
    
 
     
     
+
    
+
    
+Introduction
    
+
    As of version 3.0.0, VISION now supports the analysis of scRNA-seq data with respect to a user-defined cell lineage, or phylogeny. In this case, VISION uses the relationships between cells as specified by the phylogeny, as opposed to some user-defined latent space, to conduct the autocorrelation analysis. In this vignette, we demonstrate how a user might use this variant of the VISION pipeline - which we term PhyloVision - to analyze a recently published dataset that simultaneously profiled the single-cell transcriptomes and lineages of mouse embryogenesis (Chan et al, Nature 2019).
    
+
    This tutorial begins by showing users how to create a PhyloVision object and performing analysis on it. Then, we demonstrate how this object can be passed into the Hotspot pipeline that will identify de-novo transcriptional gene sets that are autocorrelated on the tree (this is described more below and in the Spatial Hotspot vignette. Finally, we show users how to launch a report for viewing.
    
+
    
 
    
 
    
 Preliminaries
    
 
    If you have yet to install VISION, we recommend installing the package from Github to install this package. Full source code can be found at the VISION Github repository, available here.
    
-
    -require(devtools)
-install_github("YosefLab/VISION")
    
+
    require(devtools)
+install_github("YosefLab/VISION")
    
 
    Once VISION and R are installed, you may load in VISION using library(VISION).
    
-
    Hotspot is a tool for identifying informative genes (and gene modules) in a single-cell dataset. Hotspot is installed directly from the git repository using the following command:
    
+
    To enable the Hotspot analysis below, install it directly from the git repository using the following command:
    
 
    pip install git+https://github.com/yoseflab/Hotspot.git
    
+
    If you are having trouble installing Hotspot, please refer to the documentation website here.
    
 
    
-
    
+
    
 
    
-Using PhyloVision
    
-
    Running an analysis with vision consists of three steps:
    
-
      
-
    1. Creating the PhyloVision object
      2. 
-
    2. Running the phyloAnalyze function
      3. 
-
    3. Running Hotspot
      4. 
-
    4. Browsing results
      5. 
-
    
+Running PhyloVision
    
 
    First, we need to load VISION, reticulate and ape.
    
 
     knitr::opts_chunk$set(echo = TRUE)
@@ -168,17 +167,16 @@ 
    
 
 # Read the tree
 tree <- read.tree(paste(file_path, "embryo_tree.newick", sep="/"))
-# Collapse one mutations
+
+# Collapse one mutations with ape
 tree <- collapse.singles(tree)
-expr <- expr[, tree$tip.label]
 
 # Construct the Vision object
 vis <- PhyloVision(tree=tree, data=expr, signatures=sig, meta=meta, num_neighbors=30, projection_genes= rownames(expr))
    
 
    Tree
    
 
    The ape phylogeny object. Singleton edges should be collapsed prior to use. Ensure that leaf names correspond to same names used in the expression matrix.
    
 
    Expression Data
    
-
    The provided expression data should be scaled and normalized. It is recommended to apply more advanced normalization procedures such as batch correction or removal of technical confounders.
    
-
    The expression data should not be log-transformed prior to loading into VISION.
    
+
    The provided expression data should be library-normalized. The expression data should not be log-transformed prior to loading into VISION. For more information on the input to VISION, please refer to the central VISION vignette.
    
 
    Signatures
    
 
    Signatures can be provided as a list of paths to signature files (*.gmt) or Signature objects.
    
 
    See the signature vignette for more information on finding or creating gene Signatures.
    
@@ -198,10 +196,12 @@ 
    
 
    
 
    
 Running Hotspot analysis
    
-
    We can also perform Hotspot module analysis. The expression data is already logged for us.
    
+
    As mentioned above, PhyloVision can take advantage of the new Hotspot functionality in VISION. Briefly, Hotspot is a tool for inferring modules of genes that are significantly autocorrelated with one another and a particular latent space (e.g., the first 30 principal components of a gene expression matrix). When combined with PhyloVision, the Hotspot functionality will use the user-defined phylogeny as the latent space.
    
+
    We can invoke the Hotspot analysis with the function runHotspot and setting tree=True. Upon doing so, this will identify modules of genes and add these as Signatures to the VISION object for autocorrelation evaluation. Moreover, to add interpretability to this analysis, VISION will also compute the enrichment between all the user-defined Signatures and each Hotspot module. This information will be accessible on the web-based report by selecting the “Hotspot” mode in the top-right of the web-page.
    
+
    The full Hotspot API is exposed for analysis as well. For more on the Hotspot API see here. To note, while it is typically not recommended to use model="normal" and logdata=FALSE in Hotpsot, we elect to do so because the data here has been previously log-normalized. In more typical single-cell anlayses where the user is working with a library-normalized count matrix, we suggest setting model="danb" and logdata=TRUE.
    
 
     vis <- runHotspot(vis, model="normal", tree=TRUE, min_gene_threshold=50, n_neighbors = 30, number_top_genes = nrow(expr), logdata=FALSE)
    
-
    The full Hotspot API is exposed for analysis as well. For more on the Hotspot API see here
    
+
    We have additionally exposed the full Hotspot pipeline should a user want to iterate with different parameters:
    
 
     # Init Hotspot
 hs <- hsInit(vis, model = "normal", tree=TRUE, logdata=FALSE)
@@ -233,9 +233,13 @@ 
    
 
    
 
    
 Viewing Results
    
-
    Finally, we can launch the Vision browser.
    
+
    Finally, we can launch the Vision browser. If you are local, the following will work:
    
 
+
    Else, if you would like to launch from a server, you can use the following settings:
    
+
    +viewResults(vis, host='0.0.0.0', port=8100, browser=F)
    
+
    Now, the report will be visible from port 8100 from your server (e.g., http://server-name:8100/Results.html)
    
 
    
 
    
   
    
diff --git a/docs/articles/spatialHotspot.html b/docs/articles/spatialHotspot.html
index 0ddce6f1..37f87efc 100644
--- a/docs/articles/spatialHotspot.html
+++ b/docs/articles/spatialHotspot.html
@@ -124,32 +124,31 @@ 
    Spatial Data and Hotspot
    
 
     
     
+
    
+
    
+Introduction
    
+
    In this vignette, we demonstrate how to use the Hotspot pipeline in VISION to identify de-novo transcriptional gene modules and interpret them. To this end, we use Hotspot - an algorithm that identifies modules of genes that are significantly autocorrelated with one another on some latent space that can be used to define cell-cell similarity (e.g., the first 30 principal components). Qualitatively, this can be interpreted as a co-expression analysis that takes into account the distribution of gene expression values and nuanced cell-cell similarities. If you are interested in learning more about the algorithm, you can read the original publication.
    
+
    In the example below, we use spatial transcriptomic data from the Slide-seq technology for the Hotspot analysis, following the original Hotspot tutorial. Though this analysis is extensible to more typical latent spaces, this is an interesting example where we show that VISION can use spatial coordinates to define cell-cell similarities.
    
+
    
 
    
 
    
 Preliminaries
    
 
    If you have yet to install VISION, we recommend installing the package from Github to install this package. Full source code can be found at the VISION Github repository, available here.
    
-
    -require(devtools)
-install_github("YosefLab/VISION")
    
-
    Once VISION and R are installed, you may load in VISION using library(VISION).
    
-
    Hotspot is a tool for identifying informative genes (and gene modules) in a single-cell dataset. Hotspot is installed directly from the git repository using the following command:
    
+
    require(devtools)
+install_github("YosefLab/VISION")
    
+
    Once VISION and R are installed, you may load in VISION using library(VISION). Also make sure that you have installed reticulate appropriately, as this will be necessary for running Hotspot.
    
+
    You’ll also need to install Hotspot, which can be installed directly from the git repository using the following command:
    
 
    pip install git+https://github.com/yoseflab/Hotspot.git
    
 
    
 
    
 
    
 Using VISION
    
-
    Running an analysis with vision consists of three steps:
    
-
      
-
    1. Creating the VISION object
      2. 
-
    2. Running the analyze function
      3. 
-
    3. Running Hotspot
      4. 
-
    4. Browsing results
      5. 
-
    
+
    Below, we first run the VISION pipeline as usual. In addition to importing VISION, we’ll have to import reticulate for the Hotspot analaysis.
    
 
    First, we need to load VISION and reticulate.
    
 
     knitr::opts_chunk$set(echo = TRUE)
 library(VISION)
-library(reticulate)
    
+library(reticulate) # for the Hotspot analysis

    Creating a Vision Object

    @@ -173,8 +172,8 @@

    # Construct the Vision object vis <- Vision(expr, signatures=c(sig), latentSpace = pos, meta=meta) # TODO add relevant signatures

    Expression Data

    -

    The provided expression data should be scaled and normalized. It is recommended to apply more advanced normalization procedures such as batch correction or removal of technical confounders.

    -

    The expression data should not be log-transformed prior to loading into VISION.

    +

    The provided expression data should be library-normalized.

    +

    The expression data should not be log-transformed prior to loading into VISION. For more information about how to transform the expression data, refer to the central VISION vignette.

    Signatures

    Signatures can be provided as a list of paths to signature files (*.gmt) or Signature objects.

    See the signature vignette for more information on finding or creating gene Signatures.

    @@ -194,15 +193,18 @@

    Running Hotpsot analysis

    -

    We can also perform Hotspot module analysis. For more on the Hotspot API see here and the PhyloVision vignette.

    +

    Conveniently, the Hotspot analysis can be performed directly on the VISION object we just processed. To do so, we’ll use the runHotspot function which invokes the Hotspot pipeline. For more information about the analysis pipeline & Hotspot API, you can refer the documentation website here and the PhyloVision vignette.

    +

    As described in the original Hotspot vignette, we use the bernoulli model because of the low capture rate of the spatial technology. In a typical anlaysis, we would use the danb model.

     vis@params$latentSpace$projectionGenes <- rownames(vis@exprData) # Use all genes.
 vis <- runHotspot(vis, model="bernoulli", num_umi=meta["num_umi"], logdata=FALSE)
    +

    The PhyloVision vignette describes the additional API that is exposed for iterating on the Hotspot analysis.

    +

    After running the Hotpsot pipeline, the VISION object will have populated slots storing the gene modules, the scores for each cell with respect to these new gene modules, and the enrichment score between user-specified signatures and the new Hotspot gene modules. These results can be explored in the Hotspot mode of the VISION web-based report.

    Viewing results

    -

    Finally, we can launch the Vision browser.

    +

    Finally, we can launch the Vision browser. The results from the Hotspot analysis can be viewed by clicking on the “Hotspot” button on the top-right of the web report.

    diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 595060d8..64b6ce1a 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -11,7 +11,7 @@ articles: web_only/10xData: 10xData.html web_only/Seurat: Seurat.html web_only/SignatureAutocorrelation: SignatureAutocorrelation.html -last_built: 2021-08-19T18:40Z +last_built: 2021-08-30T21:44Z urls: reference: https://yoseflab.github.io/VISION//reference article: https://yoseflab.github.io/VISION//articles diff --git a/docs/reference/matrix_wilcox_cpp.html b/docs/reference/matrix_wilcox_cpp.html index 788d3291..516ce506 100644 --- a/docs/reference/matrix_wilcox_cpp.html +++ b/docs/reference/matrix_wilcox_cpp.html @@ -172,7 +172,7 @@

    C++ wilcox rank-sums test

    data, cluster_num, cluster_denom, - jobs = getOption("mc.cores", 2L) + jobs = getOption("mc.cores", 1L) )

    Arguments

    diff --git a/man/matrix_wilcox_cpp.Rd b/man/matrix_wilcox_cpp.Rd index 8208043c..2975723b 100644 --- a/man/matrix_wilcox_cpp.Rd +++ b/man/matrix_wilcox_cpp.Rd @@ -8,7 +8,7 @@ matrix_wilcox_cpp( data, cluster_num, cluster_denom, - jobs = getOption("mc.cores", 2L) + jobs = getOption("mc.cores", 1L) ) } \arguments{ From b21442f06a2b4ae60f1d23166dffb5cdf04c4711 Mon Sep 17 00:00:00 2001 From: Yanay1 Date: Mon, 30 Aug 2021 14:46:33 -0700 Subject: [PATCH 62/62] added the api doc --- docs/API.html | 634 ++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 634 insertions(+) create mode 100644 docs/API.html diff --git a/docs/API.html b/docs/API.html new file mode 100644 index 00000000..6cd6af69 --- /dev/null +++ b/docs/API.html @@ -0,0 +1,634 @@ + + + + + + + + +GET: /SessionInfo • VISION + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + + +
    + +
    +
    +
    +

    GET: /SessionInfo

    +
    + + +
    + +

    Returns high-level configuration info on this VISION session. Mostly used to enable/disable features in the visualizer.

    +
      +
    • ‘name’: A title for this session (shown in the top title bar)
      • +
    • ‘meta_sigs’: Names of meta-data signatures. Sent here as a convenience as numeric meta-data signatures and gene signatures get combined in the display and often lookups are needed to distinguish.
      • +
    • ‘ncells’: Total number of cells
      • +
    • ‘pooled’: Whether or not there is micro-pooling
      • +
    • ‘has_sigs’: Whether or not there are gene signatures
      • +
    • ‘has_proteins’: Whether or not there are CITE-seq proteins
      • +
    • ‘has_lca’: Whether or not LC Annotator analysis is available
      • +
    • ‘has_tree’: Whether or not Trajectories are available
      • +
    +

    Response structure:

    +
        {
+        'name': 'Session Name',
+        'meta_sigs': [list of string],
+        'ncells': int,
+        'pooled': bool,
+        'has_sigs': bool,
+        'has_proteins': bool,
+        'has_lca': bool,
+        'has_tree': bool,
+    }
    +
    +
    +

    +GET: /Signature/Scores/ +

    +

    Return the per-cell signature scores for signature: <sig_name> Data comes from matrix

    +

    Response structure:

    +
        {
+        'cells': [list of str,  cell ids...],
+        'values': [list of Number, per cell signature scores],
+    }
    +
    +
    +

    +GET: /Signature/Meta/ +

    +

    Return the per-cell meta-data values for variable: <sig_name> Data comes from dataframe

    +

    Response structure:

    +
        {
+        'cells': [list of str,  cell ids...],
+        'values': [list of Number or string, per-cell meta-data values],
+    }
    +
    +
    +

    +GET: /Signature/Info/ +

    +

    Returns information associated with a signature Data comes from

    +

    Response structure:

    +
        {
+        'sigDict': { # signature-gene weights
+            'GeneName1': 1, 
+            'GeneName2': -1,
+            ...
+        },
+        'name': 'Signature Name',
+        'source': 'Signature source', # typically filename where signature was loaded from
+        'metaData': 'Signature description...', # second column in .gmt file
+        'geneImportance': { # signature-gene importance values
+            'GeneName1': .1,
+            'GeneName2': .01, 
+            ...
+        }
+    }
    +
    +
    +

    +GET: /Signature/Expression// +

    +

    Returns expression values for <sig_name> grouped by <cluster_var>. This is used to generate the gene x cluster heatmap in the bottom left Values are computed on the fly at the server

    +

    Response structure

    +
    {
+    'data': list of list of Number  (2d matrix, outer index is row index)
+    'sample_labels': column labels for the matrix in 'data'
+    'gene_labels': row labels for the matrix in 'data'
+}
    +
    +
    +

    +GET: /Proteins/<protein_name>/Values

    +

    Returns the per-cell protein expression values for <protein_name> Data comes from matrix

    +

    Response structure:

    +
        {
+        'cells': [list of str,  cell ids...],
+        'values': [list of Number, per cell protein expression],
+    }
    +
    +
    +

    +GET: /FilterGroup/SigClusters/Normal

    +

    For each signature, describes the assignment of signatures to signature-clusters This is used to group signatures in the upper-left section

    +

    Response structure:

    +
    {
+    "Signature Name" (str): <cluster_number> (int),
+    ...
+}
    +
    +
    +

    +GET: /FilterGroup/SigClusters/Proteins

    +

    For each protein, describes the assignment of proteins to protein-clusters Proteins aren’t actually clustered in the interface. Every protein is assigned to cluster #1

    +

    Response structure:

    +
    {
+    "Protein Name" (str): 1,
+    ...
+}
    +
    +
    +

    +GET: /FilterGroup/SigClusters/Meta

    +

    For each meta-data variable, describes the assignment of each variable to meta-data clusters This is used when micropools are created to group factor variables with their expanded percent-value-per-micropool representations

    +

    Response structure:

    +
    {
+    "Metadata variable Name" (str): <cluster_number> (int),
+    ...
+}
    +
    +
    +

    +GET: /Projections//coordinates/ +

    +

    Returns the coordinates for projection <proj_name> in column <proj_col> Since the scatter plot can show more than just projects, this has been expanded to also return coordinates from the latent space or other meta-data variables. <proj_name> can come from names in , or can be “Meta Data” to refer to or “Latent Space” to refer to . In either case <proj_name> should refer to an associated column.

    +

    Response structure:

    +

    List of list of [coordinate, 'cell id']

    +
    [
+    [coordinate (float): 'cell id' (str)],
+    [coordinate (float): 'cell id' (str)],
+    [coordinate (float): 'cell id' (str)],
+    ...
+[
    +
    +
    +

    +GET: /Projections/list

    +

    Returns information on projections and other variables that can be plotted in the main scatter-plot panel. Used to create the dropdown menus.

    +

    Response structure:

    +

    Dictionary where keys are the name of projections/meta data/latent space and the values are a list of the associated columns

    +
    {
+    'projection_name_1': list of column names in the projection,
+    'projection_name_2': list of column names in the projection,
+    'Meta Data': list of numeric meta-data variables,
+    'Latent Space': list of column names in the latent space
+}
    +
    +
    +

    +GET: /PearsonCorr/Normal

    +

    Gets information for the LC Annotator - the correlation of each signature with each latent component

    +

    Response structure:

    +
    {
+    "zscores": list of list of correlation coefficients (N signatures x N components),
+    "pvals": list of list of p-values (N signatures x N components),
+    "proj_labels": list of latent space column names in the same order as columns of 'zscores'/'pvals',
+    "sig_labels": list of signature names in the same order as columns of 'zscores'/'pvals',
+}
    +
    +
    +

    +GET: /PearsonCorr/Proteins

    +

    Gets information for the LC Annotator - the correlation of each protein with each latent component

    +

    Response structure:

    +
    {
+    "zscores": list of list of correlation coefficients (N proteins x N components),
+    "pvals": list of list of p-values (N proteins x N components),
+    "proj_labels": list of latent space column names in the same order as columns of 'zscores'/'pvals',
+    "sig_labels": list of proteins names in the same order as columns of 'zscores'/'pvals',
+}
    +
    +
    +

    +GET: /PearsonCorr/Meta

    +

    Gets information for the LC Annotator - the correlation of each numeric meta-data variable with each latent component

    +

    Response structure:

    +
    {
+    "zscores": list of list of correlation coefficients (N variables x N components),
+    "pvals": list of list of p-values (N variables x N components),
+    "proj_labels": list of latent space column names in the same order as columns of 'zscores'/'pvals',
+    "sig_labels": list of variables names in the same order as columns of 'zscores'/'pvals',
+}
    +
    +
    +

    +POST: /DE

    +

    Requests a differential expression analysis from the server.

    +

    Determines the set of cells used for the numerator (i.e. _num or _n) and for the denominator (i.e. _denom or _d)

    +

    Examples:

    +
      +
    • To select cells in cluster 5 for the numerator set 'type_n': 'meta', 'subtype_n': 'cluster', 'group_num': 'Cluster 5' +
      • +
    • To select cells in a saved manual selection for the numerator set 'type_n': 'saved_selection', 'group_num': 'name_of_selection' +
      • +
    • To select a specific set of cell ids for the numerator set 'type_n': 'current', 'group_num': list of cell ids +
      • +
    +

    Posted data structure:

    +
    {
+    'type_n': either 'current', 'meta', or 'saved_selection'
+    'type_d':  either 'remainder', 'meta', or 'saved_selection'
+    'subtype_n': which meta-data variable to group cells by if type_n is 'meta'
+    'subtype_d': which meta-data variable to group cells by if type_d is 'meta'
+    'group_num': list of cell ids (if type_n is 'current') OR name of saved selection (if type_n is 'saved_selection')
+                 OR value of categorical meta-data variable (if type_n is 'meta')
+    'group_denom': same behavior as 'group_num'
+    'min_cells': (int) pre-filter genes expressed in less than this many cells
+    'subsample_groups': (bool), whether or not to subsample each comparison group first
+    'subsample_N': (int) size of the groups after subsampling.  Ignored if 'subsample_groups' is false
+}
    +

    Response structure:

    +

    DE Results table with {‘column name’ -> list of values}

    +
    {
+    'Feature': list of feature (gene or protein) names
+    'Type': list of either 'Gene' or 'Protein' 
+    'logFC': list of log-fold-change values
+    'stat': list of AUC values
+    'pval': list of FDR-corrected p-values
+}
    +
    +
    +

    +GET: /Clusters/MetaLevels

    +

    The display of the top-left area for signatures/proteins/meta-data depends on the selected grouping variable in the dropdown. Commands scoped to a particular grouping variable are nested under “/Clusters”.

    +

    This call returns a list of grouping variables and the levels/categories associated with them.

    +

    Response structure:

    +
        {
+        'name of variable': [list of str - values this variable can take],
+        'name of variable': [list of str - values this variable can take],
+        'Cell Type': ['CD4+', 'CD8+', 'NK'],   # For example
+    }
    +
    +
    +

    +GET: /Clusters//SigProjMatrix/Normal +

    +

    Returns matrices consisting of test statistic and p-value for 1 vs. all differential signature tests and for local autocorrelation.

    +

    First column is “Score” and values are for local autocorrelation. Statistic is the 1 - Geary’s C.

    +

    Other columns are for 1 vs. all differential signature tests for each value in the selected grouping variable in the dropdown. Test statistic are the AUC values from a ranksums test. P-values also from this test.

    +

    Response structure:

    +
        {
+        'sig_labels': [list of str]  # Rows of matrices in zscores and pvals
+        'proj_labels': [list of str] # Columns of the matrices in zscores and pvals
+        'zscores': [list of list of number]  # signatures x cell group (+ 'Score') matrix of test statistics
+        'pvals': [list of list of number] # signatures x cell group (+ 'Score') matrix of p-values
+    }
    +
    +
    +

    +GET: /Clusters//SigProjMatrix/Meta +

    +

    Same as /Clusters/<cluster_variable>/SigProjMatrix/Normal, but for meta-data variables

    +

    Response structure:

    +
        {
+        'sig_labels': [list of str]  # Rows of matrices in zscores and pvals
+        'proj_labels': [list of str] # Columns of the matrices in zscores and pvals
+        'zscores': [list of list of number]  # variables x cell group (+ 'Score') matrix of test statistics
+        'pvals': [list of list of number] # variables x cell group (+ 'Score') matrix of p-values
+    }
    +
    +
    +

    +GET: /Clusters//ProteinMatrix +

    +

    Same as /Clusters/<cluster_variable>/SigProjMatrix/Normal, but for CITE proteins

    +

    Response structure:

    +
        {
+        'sig_labels': [list of str]  # Rows of matrices in zscores and pvals
+        'proj_labels': [list of str] # Columns of the matrices in zscores and pvals
+        'zscores': [list of list of number]  # proteins x cell group (+ 'Score') matrix of test statistics
+        'pvals': [list of list of number] # proteins x cell group (+ 'Score') matrix of p-values
+    }
    +
    +
    +

    +GET: /Clusters/list

    +

    Not used anymore

    +
    +
    +

    +GET: /Clusters//Cells +

    +

    Not used anymore

    +
    +
    +

    +GET: /Expression/Genes/List

    +

    Retrieves a list of genes for which expression values can be plotted. Used to populate the dropdown in the ‘Genes’ tab.

    +

    Response structure:

    +
    [list of str - gene names]
    +
    +
    +

    +GET: /Expression/Gene/ +

    +

    Gets the per-cell expression of the gene specified by <gene_name>. Expression values returned are on a log2 scale.

    +

    Response structure: Items in ‘values’ correspond to the cells in ‘cells’ in order

    +
        {
+        'cells': [list of str - cell identifiers],
+        'values': [list of number - gene expression values],
+    }
    +
    +
    +

    +GET: /Cell//Meta +

    +

    Retrieves meta-data information for an individual cell specified by <cell_id>

    +

    Response structure:

    +
        {
+        'variable name': value (str or number),
+        'variable name': value (str or number),
+        'variable name': value (str or number),
+        ...
+    }
    +
    +
    +

    +POST: /Cells/Meta

    +

    Retrieves meta-data information for a group of cells

    +

    Posted data structure

    +
    [list of cell id]
    +

    Response structure:

    +
        {
+        'numeric': {
+            '<variable name>': {
+                'Min': <min value>,
+                'Median': <median value>,
+                'Max': <max value>,
+            },
+            '<variable name>': {
+                'Min': <min value>,
+                'Median': <median value>,
+                'Max': <max value>,
+            },
+            # Repeat for additional numeric meta-data variables
+        },
+        'factor': {
+            '<variable name>': {
+                '<factor level 1>': number (proportion of cells assigned to this level,
+                '<factor level 2>': number (proportion of cells assigned to this level,
+                '<factor level 3>': number (proportion of cells assigned to this level,
+                ...
+            }
+            # Repeat for additional factor meta-data variables
+        }
+    }
    +
    +
    +

    +GET: /Cells/Selections

    +

    Used when loading a selection of cells.

    +

    Response structure:

    +
    [list of str - names of saved selections]
    +
    +
    +

    +GET: /Cells/Selections/ +

    +

    Retrieves the cells associated with the selection, <selection_id>

    +

    Response structure:

    +
    [list of str - cell ids in the indicated cell selection]
    +
    +
    +

    +POST: /Cells/Selections/ +

    +

    Saves a cell selection with name <selection_id>

    +
    [list of str - cell ids to be assigned to this cell selection]
    +
    +
    +

    +GET: /Tree/Projections/list

    +

    Get the list of different tree layouts that are available Used to populate the ‘Projection’ dropdown under the ‘Trajectories’ view

    +

    R version: returns the names of

    +

    Response structure:

    +
    [list of str - names of tree projections]
    +
    +
    +

    +GET: /Tree/Projections//coordinates +

    +

    Returns the coordinates for the tree layout <proj_name> in addition to the position of individual cells

    +

    Response structure:

    +
        [
+        [
+            [<x val>, <y val>, <cell id>],  # coordinates for individual cells
+            [<x val>, <y val>, <cell id>],
+            [<x val>, <y val>, <cell id>],
+            ...
+        ],
+        [
+            [<x val>, <y val>],  # coordinates for internal tree nodes
+            [<x val>, <y val>], 
+            [<x val>, <y val>], 
+            ...
+        ],
+        [list of list of number]  # 0/1 adjacency matrix for internal tree nodes
+    ]
    +
    +
    +

    +GET: /Tree/SigProjMatrix/Normal

    +

    Returns matrices consisting of test statistic and p-value trajectory autocorrelation Format is similar to /Clusters/<cluster_variable>/SigProjMatrix/Normal, but without the 1 vs all test results.

    +

    ‘zscores’ and ‘pvals’ matrices have just a single column

    +

    Response structure:

    +
        {
+        'sig_labels': [list of str]  # Rows of matrices in zscores and pvals
+        'proj_labels': ["Score"],
+        'zscores': [list of list of number]  # signatures x 1 matrix of test statistics
+        'pvals': [list of list of number] # signatures x 1 matrix of p-values
+    }
    +
    +
    +

    +GET: /Tree/SigProjMatrix/Meta

    +

    Same as /Tree/SigProjMatrix/Normal but for meta-data variables

    +

    ‘zscores’ and ‘pvals’ matrices have just a single column

    +

    Response structure:

    +
        {
+        'sig_labels': [list of str]  # Rows of matrices in zscores and pvals
+        'proj_labels': ["Score"],
+        'zscores': [list of list of number]  # variables x 1 matrix of test statistics
+        'pvals': [list of list of number] # variables x 1 matrix of p-values
+    }
    +
    +
    +

    +GET: /Tree/ProteinMatrix

    +

    Same as /Tree/SigProjMatrix/Normal but for CITE protein expression values

    +

    ‘zscores’ and ‘pvals’ matrices have just a single column

    +

    Response structure:

    +
        {
+        'sig_labels': [list of str]  # Rows of matrices in zscores and pvals
+        'proj_labels': ["Score"],
+        'zscores': [list of list of number]  # proteins x 1 matrix of test statistics
+        'pvals': [list of list of number] # proteins x 1 matrix of p-values
+    }
    +
    + + +
    + + + +
    + + + + +
    + + + + + + + +