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ComplexHeatmap

Complex heatmaps are efficient in visualizing associations between different sources of data sets and revealing potential patterns. Here the ComplexHeatmap package provides a highly flexible way to arrange multiple heatmaps and supports various annotation graphics.

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Cite this software

DOI:

10.5281/zenodo.13820907

Description

Make Complex Heatmaps

Complex heatmaps are efficient to visualize associations between different
sources of data sets and reveal potential patterns. Here the
ComplexHeatmap package provides a highly flexible way to arrange multiple
heatmaps and supports various annotation graphics.

The InteractiveComplexHeatmap package can directly export static complex heatmaps into an interactive Shiny app. Have a try!

Citation

Zuguang Gu, et al., Complex heatmaps reveal patterns and correlations in multidimensional genomic data, Bioinformatics, 2016.

Zuguang Gu. Complex Heatmap Visualization, iMeta, 2022.

Install

ComplexHeatmap is available on Bioconductor, you can install it by:

if (!requireNamespace("BiocManager", quietly=TRUE))
    install.packages("BiocManager")
BiocManager::install("ComplexHeatmap")

If you want the latest version, install it directly from GitHub:

library(devtools)
install_github("jokergoo/ComplexHeatmap")

Usage

Make a single heatmap:

Heatmap(mat, ...)

A single Heatmap with column annotations:

ha = HeatmapAnnotation(df = anno1, anno_fun = anno2, ...)
Heatmap(mat, ..., top_annotation = ha)

Make a list of heatmaps:

Heatmap(mat1, ...) + Heatmap(mat2, ...)

Make a list of heatmaps and row annotations:

ha = HeatmapAnnotation(df = anno1, anno_fun = anno2, ..., which = "row")
Heatmap(mat1, ...) + Heatmap(mat2, ...) + ha

Documentation

The full documentations are available at https://jokergoo.github.io/ComplexHeatmap-reference/book/ and the website is at https://jokergoo.github.io/ComplexHeatmap.

Blog posts

There are following blog posts focusing on specific topics:

Examples

Visualize Methylation Profile with Complex Annotations

complexheatmap_example4

Correlations between methylation, expression and other genomic features

complexheatmap_example3

Visualize Cell Heterogeneity from Single Cell RNASeq

complexheatmap_example2

Making Enhanced OncoPrint

complexheatmap_example1

UpSet plot

3D heatmap

image

License

MIT @ Zuguang Gu

Logo of ComplexHeatmap
Keywords
bioconductor
Clustering
Data Science
Data Visualization
FAIR Data
Omics
Programming language
  • R 100%
License
  • MIT
</>Source code
Packages
bio

Participating organisations

German Cancer Research Center

Reference papers

Mentions

Contributors

ZG
Zuguang Gu
Developer
German Cancer Research Center