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README.md
# Make Complex Heatmaps <a href="https://jokergoo.github.io/ComplexHeatmap-reference/book/"><img src="https://jokergoo.github.io/ComplexHeatmap-reference/book/complexheatmap-cover.jpg" width=240 align="right" style="border:2px solid black;" ></a> [![Build Status](https://travis-ci.org/jokergoo/ComplexHeatmap.svg)](https://travis-ci.org/jokergoo/ComplexHeatmap) [![codecov](https://img.shields.io/codecov/c/github/jokergoo/ComplexHeatmap.svg)](https://codecov.io/github/jokergoo/ComplexHeatmap) [![bioc](http://www.bioconductor.org/shields/downloads/devel/ComplexHeatmap.svg)](https://bioconductor.org/packages/stats/bioc/ComplexHeatmap/) [![bioc](http://www.bioconductor.org/shields/years-in-bioc/ComplexHeatmap.svg)](http://bioconductor.org/packages/devel/bioc/html/ComplexHeatmap.html) <img src="http://jokergoo.github.io/complexheatmap_logo.svg" width="550"> 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](http://bioinformatics.oxfordjournals.org/content/early/2016/05/20/bioinformatics.btw313.abstract), Bioinformatics, 2016 ## Install `ComplexHeatmap` is available on [Bioconductor](http://www.bioconductor.org/packages/devel/bioc/html/ComplexHeatmap.html), 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 ``` ## 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](https://jokergoo.github.io/2020/05/06/translate-from-pheatmap-to-complexheatmap/) - [Set cell width/height in the heatmap](https://jokergoo.github.io/2020/05/11/set-cell-width/height-in-the-heatmap/) - [Interactive ComplexHeatmap](https://jokergoo.github.io/2020/05/15/interactive-complexheatmap/) - [Word cloud as heatmap annotation](https://jokergoo.github.io/2020/05/31/word-cloud-as-heatmap-annotation/) - [Which heatmap function is faster?](https://jokergoo.github.io/2020/06/19/which-heatmap-function-is-faster/) - [Rasterization in ComplexHeatmap](https://jokergoo.github.io/2020/06/30/rasterization-in-complexheatmap/) - [Block annotation over several slices](https://jokergoo.github.io/2020/07/06/block-annotation-over-several-slices/) - [Integrate ComplexHeatmap with cowplot package](https://jokergoo.github.io/2020/07/14/integrate-complexheatmap-with-cowplot-package/) ## Examples ### Visualize Methylation Profile with Complex Annotations ![complexheatmap_example4](https://user-images.githubusercontent.com/449218/47718635-2ec22980-dc49-11e8-9f01-37becb19e0d5.png) ### Correlations between methylation, expression and other genomic features ![complexheatmap_example3](https://user-images.githubusercontent.com/449218/47718636-2ec22980-dc49-11e8-8db0-1659c27dcf40.png) ### Visualize Cell Heterogeneity from Single Cell RNASeq ![complexheatmap_example2](https://user-images.githubusercontent.com/449218/47718637-2ec22980-dc49-11e8-925e-955c16cfa982.png) ### Making Enhanced OncoPrint ![complexheatmap_example1](https://user-images.githubusercontent.com/449218/47718638-2ec22980-dc49-11e8-845e-21e51d3b8e73.png) ### UpSet plot ![](https://pbs.twimg.com/media/Dvpp31uX4AAqGDP.jpg) ### Interactive heatmaps Heatmaps can be exported into a Shiny app by `ht_shiny(ht)`. See examples at https://jokergoo.shinyapps.io/interactive_complexheatmap/. <img src="https://user-images.githubusercontent.com/449218/82199376-e5eec600-98fd-11ea-9fca-ad95d405dc20.gif" /> ## License MIT @ Zuguang Gu