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!
Zuguang Gu, et al., 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, ...) + haThe 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:
- Make 3D heatmap
- 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
MIT @ Zuguang Gu