PyComplexHeatmap

PyComplexHeatmap is a python package to plot complex heatmap (clustermap) with biological data.

Contents:

• Installation
  • Dependencies
  • How to install?
• Get Started
  • 1. Import packages
  • 2. Plot heatmap annotations
  • 3. Plot the heatmap with rows and columns split
  • 4. Plot the annotations along side with main heatmap
• Clustermap
  • A quick example
  • Plotting annotations
  • Top, bottom, left ,right annotations
• dotHeatmap
  • Load an example brain networks dataset from seaborn
  • Plot traditional heatmap using square marker marker='s'
  • Simple dot heatmap using fixed dot size
  • Changing the size of point
  • Add parameter hue and use different colors for different groups
  • Add parameter hue and use different cmap and marker for different groups
  • Plot clustermap using seaborn brain networks dataset
  • Visualize up to five dimension data using DotClustermapPlotter
  • Visualizing gene set enrichment analysis results (clusterProfiler) using dotHeatmap
• oncoPrint
  • oncoPrint: visualizing TCGA Lung Adenocarcinoma Carcinoma Variants Dataset
  • Visualizing categorical variables using oncoPrint
• Advanced Usage
  • Generate dataset
  • Add selected rows labels
  • Add annotations on the top of heatmap cells
  • Only plot the annotations
  • Change orentation to down and add extra space
  • Change orentation to the left
  • Change orentation to the right
  • Changing orientation using parameter orientation
  • Add multiple heatmap annotations using for loop
  • Cluster between groups and cluster within groups
  • Custom annotation
  • Custom linkage
  • Image annotation
  • How to force display all row/col ticklabels?
• More Examples
  • Visualizing Differential Expression Genes
  • Visualizing Single Cell DNA Methylation Data (Loyfer2023)
  • Composite two heatmaps horizontally for mouse DNA methylation array dataset
  • Plot correlation matrix for CpG modules using DotClustermap
• Kwargs
  • label_kws, xticklabels_kws and yticklabels_kws: Modifying the heatmap annotations labels and xticklabels, yticklabels
  • xlabel_kws and ylabel_kws: Modifying xlabel and ylabel
  • Control gap & pad in heatmap
  • How to remove arrow in anno_label
• colormap
  • Default matplotlib colormaps
  • Build-in colormaps (Not included in matplotlib default cmaps)
  • How to use the Build-in cmap?
• Gallery
• For Developers
  • Understand the layout:
  • Bezier dendrogram
  • anno_label
  • anno_img
  • Color palette design
• PyComplexHeatmap
  • PyComplexHeatmap package
  • setup module
• Citation

Credits and Thanks

The package was provided by Wubin Ding.