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.

Citation

Zuguang Gu, Roland Eils and Matthias Schlesner, Complex heatmaps reveal patterns and correlations in multidimensional genomic data, Bioinformatics, 2016

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:

• Translate from pheatmap to ComplexHeatmap
• Set cell width/height in the heatmap
• Interactive ComplexHeatmap
• Word cloud as heatmap annotation
• Which heatmap function is faster?
• Rasterization in ComplexHeatmap
• Block annotation over several slices
• Integrate ComplexHeatmap with cowplot package

Examples

Visualize Methylation Profile with Complex Annotations

Correlations between methylation, expression and other genomic features

Visualize Cell Heterogeneity from Single Cell RNASeq

Making Enhanced OncoPrint

UpSet plot

Interactive heatmaps

Heatmaps can be exported into a Shiny app by ht_shiny(ht). See examples at https://jokergoo.shinyapps.io/interactive_complexheatmap/.

License

MIT @ Zuguang Gu