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
Documentation
The full documentations are available at https://jokergoo.github.io/ComplexHeatmap-reference/book/.
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
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
License
MIT @ Zuguang Gu