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
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PYPI
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Wiki

wiki/layout
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wiki/Parameters
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wiki/Features

Dependencies:

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• 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
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DOI: 10.1002/imt2.115
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PMID: 38454967

Installation

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1. Install using pip:

shellCopy
pip install PyComplexHeatmap

#upgrade from older version
pip install --upgrade PyComplexHeatmap

2. Install the developmental version directly from github:

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

OR

shellCopy
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

<table> <tr style="height: 500px"> <td style="width:33%; background-color:white;text-align:center; vertical-align:middle"> <a href="https://dingwb.github.io/PyComplexHeatmap/build/html/notebooks/kwargs.html#Control-gap-&-pad-in-heatmap"> <img src="docs/images/gallery1.png" title="kwargs, gap and pad" align="center" width="250px"> </a> </td> <td style="width:33%; background-color:white;text-align:center; vertical-align:middle"> <a href="https://dingwb.github.io/PyComplexHeatmap/build/html/notebooks/anno_img_example.html#Visualizing-motif-enrichment-results-using-anno_img"> <img src="docs/images/gallery11.png" title="Modify labels" align="center" width="250px"> </a> </td> <td style="width:33%; background-color:white;text-align:center; vertical-align:middle"> <a href="https://dingwb.github.io/PyComplexHeatmap/build/html/notebooks/composite_heatmaps.html#Composite-two-heatmaps-horizontally-for-mouse-DNA-methylation-array-dataset"> <img src="docs/images/gallery3.png" title="Combine two heatmap horizontally" align="center" width="250px"> </a> </td> </tr> <tr style="height: 500px"> <td style="width:33%; background-color:white;text-align:center; vertical-align:middle"> <a href="https://dingwb.github.io/PyComplexHeatmap/build/html/notebooks/advanced_usage.html#Only-plot-the-annotations"> <img src="docs/images/gallery5.png" title="Only plot annotations" align="center" width="250px"> </a> </td> <td style="width:33%; background-color:white;text-align:center; vertical-align:middle"> <a href="https://dingwb.github.io/PyComplexHeatmap/build/html/notebooks/advanced_usage.html#Cluster-between-groups-and-cluster-within-groups"> <img src="docs/images/gallery6.png" title="Cluster between groups" align="center" width="250px"> </a> </td> <td style="width:33%; background-color:white;text-align:center; vertical-align:middle"> <a href="https://dingwb.github.io/PyComplexHeatmap/build/html/notebooks/single_cell_methylation.html"> <img src="docs/images/gallery9.png" title="DNA methylation cell type specific signatures" align="center" width="250px"> </a> </td> </tr> <tr style="height: 500px"> <td style="width:33%; background-color:white;text-align:center; vertical-align:middle"> <a href="https://dingwb.github.io/PyComplexHeatmap/build/html/notebooks/oncoPrint.html"> <img src="docs/images/gallery8.png" title="OncoPrint with columns split" align="center" width="250px"> </a> </td> <td style="width:33%; background-color:white;text-align:center; vertical-align:middle"> <a href="https://dingwb.github.io/PyComplexHeatmap/build/html/notebooks/dotHeatmap.html#Visualize-up-to-five-dimension-data-using-DotClustermapPlotter"> <img src="docs/images/gallery7.png" title="Dot clustermap to show enrichment result" align="center" width="250px"> </a> </td> <td style="width:33%; background-color:white;text-align:center; vertical-align:middle"> <a href="https://dingwb.github.io/PyComplexHeatmap/build/html/notebooks/oncoPrint2.html"> <img src="docs/images/gallery4.png" title="Visualizing categorical variables using oncoPrint" align="center" width="250px"> </a> </td> </tr> <tr style="height: 500px"> <td style="width:33%; background-color:white;text-align:center; vertical-align:middle"> <a href="https://dingwb.github.io/PyComplexHeatmap/build/html/notebooks/cpg_modules.html#Plotting-the-Dot-clustermap"> <img src="docs/images/gallery2.png" title="Dot clustermap with annotations" align="center" width="250px"> </a> </td> <td style="width:33%; background-color:white;text-align:center; vertical-align:middle"> <a href="https://dingwb.github.io/PyComplexHeatmap/build/html/notebooks/advanced_usage.html#Custom-annotation"> <img src="docs/images/gallery10.png" title="Custom annotation" align="center" width="250px"> </a> </td> <td style="width:33%; background-color:white;text-align:center; vertical-align:middle"> <a href="https://dingwb.github.io/PyComplexHeatmap/build/html/notebooks/gene_enrichment_analysis.html#Plot"> <img src="docs/images/gallery12.png" title="Plot only the annotation with different orientations" align="center" width="250px"> </a> </td> </tr> </table>

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.