Make Complex Heatmaps (original) (raw)

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.

Install

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

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

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

{r} library(devtools) install_github("jokergoo/ComplexHeatmap")

Usage

Make a single heatmap:

{r} Heatmap(mat, ...)

A single Heatmap with column annotations:

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

Make a list of heatmaps:

{r} Heatmap(mat1, ...) + Heatmap(mat2, ...)

Make a list of heatmaps and row annotations:

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

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