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.

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

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")

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

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

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

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

MIT @ Zuguang Gu