plotly / dash-bio

Open-source bioinformatics components for Dash
https://dash-gallery.plotly.host/Portal/?search=Bioinformatics
MIT License
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Feature request: Support for string type chromosome column in `ManhattanPlot` #772

Open LawrenceLiu023 opened 1 month ago

LawrenceLiu023 commented 1 month ago

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