PyComplexHeatmap

PyComplexHeatmap

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

Documentation:

https://dingwb.github.io/PyComplexHeatmap

PYPI

Wiki

wiki/layout
wiki/Parameters
wiki/Features

Dependencies:

• matplotlib
• numpy
• pandas
• scipy
• fastcluster (optional)

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
PMID: 38454967

Installation

• Install using pip:

pip install PyComplexHeatmap

#upgrade from older version
pip install --upgrade PyComplexHeatmap

• Install the developmental version directly from github:

pip install git+https://github.com/DingWB/PyComplexHeatmap
# reinstall
pip uninstall -y PyComplexHeatmap && pip install git+https://github.com/DingWB/PyComplexHeatmap

OR

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

Usage

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

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 ([e-mail]).

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.