PyComplexHeatmap

PyComplexHeatmap is a Python package to plot complex heatmap (clustermap). Please click here for documentation.

Documentation:

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https://dingwb.github.io/PyComplexHeatmap

PYPI

Wiki

wiki/layout
wiki/Parameters
wiki/Features

Dependencies:

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• matplotlib>=3.3.1
• numpy
• pandas
• scipy
• fastcluster

pip install --ignore-install matplotlib numpy pandas fastcluster

Citation

Ding, W., Goldberg, D. and Zhou, W. (2023), PyComplexHeatmap: A Python package to visualize multimodal genomics data. iMeta e115. https://doi.org/10.1002/imt2.115
DOI: 10.1002/imt2.115

Installation

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1. Install using pip:

pip install PyComplexHeatmap

#upgrade from older version
pip install --upgrade PyComplexHeatmap

2. Install the developmental version directly from github:

pip install git+https://github.com/DingWB/PyComplexHeatmap

if you have installed it previously and want to update it, please run pip uninstall PyComplexHeatmap and install from github again OR

git clone https://github.com/DingWB/PyComplexHeatmap
cd PyComplexHeatmap
python setup.py install

Usage

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Simple Guide To Get started

Example output

Click picture to view the source code

Advanced Usage

Kwargs

More Examples

https://dingwb.github.io/PyComplexHeatmap/build/html/more_examples.html

Call for Contributions

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The PyComplexHeatmap project welcomes your expertise and enthusiasm!

Small improvements or fixes are always appreciated. If you are considering larger contributions to the source code, please contact us (ding.wu.bin.gm@gmail.com).

Writing code isn’t the only way to contribute to PyComplexHeatmap. You can also:

• review pull requests
• help us stay on top of new and old issues
• develop tutorials, presentations, and other educational materials
• maintain and improve our website
• develop graphic design for our brand assets and promotional materials
• translate website content
• help with outreach and onboard new contributors
• put forward some new ideas about update.