Feature request: Support for string type chromosome column in ManhattanPlot #772
Description
Description
Currently the chromosome column specified with dash_bio.ManhattanPlot(chrm='<The column of chromosome>') does not support non-numeric types.
To Reproduce
Python code:
import dash_bio
plotly_demo_manhattan_path: Path = Path("../dev/data/plotly_manhattan_data.csv")
plotly_demo_manhattan_data_df: pd.DataFrame = pd.read_csv(
plotly_demo_manhattan_path, header=0, index_col=None, sep=","
)
plotly_demo_manhattan_data_df = plotly_demo_manhattan_data_df.assign(
CHR=plotly_demo_manhattan_data_df["CHR"].astype(str)
)
manhattan_plot = dash_bio.ManhattanPlot(
plotly_demo_manhattan_data_df,
chrm="CHR",
)The output:
File ~/micromamba/envs/temp/lib/python3.12/site-packages/dash_bio/component_factory/_manhattan.py:221, in _ManhattanPlot.__init__(self, x, chrm, bp, p, snp, gene, annotation, logp)
[219] else:
[220] if not is_numeric_dtype(x[chrm].dtype):
--> [221] raise TypeError("%s column should be numeric. Do you have "
[222] "'X', 'Y', 'MT', etc? If so change to "
[223] "numbers and try again." % chrm)
[225] if bp not in x.columns.values:
[226] raise KeyError("Column %s not found in 'x' data.frame" % bp)
TypeError: CHR column should be numeric. Do you have 'X', 'Y', 'MT', etc? If so change to numbers and try again.
Expected behavior
If string type for chromosomes is supported, it would allow for the creation of Manhattan plots for a greater variety of chromosomes. Additionally, this feature would enable the plotting of data from more species.
Python version: 3.12.4
Python environment (all installed packages in your current environment):
Package Version
------------------------- ---------
annotated-types 0.7.0
asttokens 2.4.1
attrs 24.2.0
beautifulsoup4 4.12.3
biopython 1.84
bioreport 1.1.5
black 24.8.0
blinker 1.8.2
Brotli 1.1.0
bs4 0.0.2
certifi 2024.7.4
cffi 1.17.0
charset-normalizer 3.3.2
click 8.1.7
CNVpytor 1.3.1
colorama 0.4.6
coloredlogs 15.0.1
colormath 3.0.0
colour 0.1.5
comm 0.2.2
contourpy 1.2.1
cycler 0.12.1
dash 2.17.1
dash-bio 1.0.2
dash-core-components 2.0.0
dash-html-components 2.0.0
dash-table 5.0.0
debugpy 1.8.5
decorator 5.1.1
exceptiongroup 1.2.2
executing 2.0.1
fastjsonschema 2.20.0
Flask 3.0.3
fonttools 4.53.1
GEOparse 2.0.4
gnureadline 8.2.10
h2 4.1.0
h5py 3.11.0
hpack 4.0.0
humanfriendly 10.0
humanize 4.10.0
hyperframe 6.0.1
idna 3.8
importlib_metadata 8.4.0
importlib_resources 6.4.3
ipykernel 6.29.5
ipython 8.26.0
ipywidgets 8.1.5
itsdangerous 2.2.0
jedi 0.19.1
Jinja2 3.1.4
joblib 1.4.2
jsonschema 4.23.0
jsonschema-specifications 2023.12.1
jupyter_client 8.6.2
jupyter_core 5.7.2
jupyterlab_widgets 3.0.13
kaleido 0.2.1
kiwisolver 1.4.5
Markdown 3.6
markdown-it-py 3.0.0
MarkupSafe 2.1.5
matplotlib 3.9.2
matplotlib-inline 0.1.7
mdurl 0.1.2
multiqc 1.24.1
mypy-extensions 1.0.0
nbformat 5.10.4
nest_asyncio 1.6.0
networkx 3.3
numpy 1.26.4
packaging 24.1
pandas 2.2.2
ParmEd 4.2.2
parso 0.8.4
pathspec 0.12.1
patsy 0.5.6
periodictable 1.5.2
pexpect 4.9.0
pickleshare 0.7.5
pillow 10.4.0
pip 24.2
pip-search 0.0.12
pkgutil_resolve_name 1.3.10
platformdirs 4.2.2
plotly 5.23.0
polars 1.2.1
prompt_toolkit 3.0.47
psutil 6.0.0
ptyprocess 0.7.0
pure_eval 0.2.3
pyaml_env 1.2.1
pyarrow 17.0.0
pycparser 2.22
pydantic 2.8.2
pydantic_core 2.20.1
Pygments 2.18.0
pyparsing 3.1.4
pysam 0.22.1
PySocks 1.7.1
python-dateutil 2.9.0
pytz 2024.1
PyYAML 6.0.2
pyzmq 26.1.1
referencing 0.35.1
requests 2.32.3
retrying 1.3.3
rich 13.7.1
rich-click 1.8.3
rpds-py 0.20.0
scikit-learn 1.5.1
scipy 1.14.0
setuptools 72.1.0
six 1.16.0
soupsieve 2.6
spectra 0.0.11
stack-data 0.6.2
statsmodels 0.14.2
tenacity 9.0.0
threadpoolctl 3.5.0
tornado 6.4.1
tqdm 4.66.5
traitlets 5.14.3
typeguard 4.3.0
typing_extensions 4.12.2
tzdata 2024.1
urllib3 2.2.2
wcwidth 0.2.13
Werkzeug 3.0.4
wheel 0.44.0
widgetsnbextension 4.0.13
XlsxWriter 3.2.0
zipp 3.20.0
zstandard 0.23.0