<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>
 

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 [![bioc](http://mcube.nju.edu.cn/cgi-bin/zuguanggu/bioc_download.pl?package=ComplexHeatmap&)](https://bioconductor.org/packages/stats/bioc/ComplexHeatmap/) 

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 ## 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](http://bioinformatics.oxfordjournals.org/content/early/2016/05/20/bioinformatics.btw313.abstract), Bioinformatics, 2016
 

 ### Documentation

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

 ### 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

 ```
 

 ### 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:large)
 

 ### License
 

 MIT @ Zuguang Gu