# 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>
[](https://github.com/jokergoo/ComplexHeatmap/actions)
[](https://codecov.io/github/jokergoo/ComplexHeatmap)
[](https://bioconductor.org/packages/stats/bioc/ComplexHeatmap/)
[](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.
The [**InteractiveComplexHeatmap**](https://github.com/jokergoo/InteractiveComplexHeatmap) package can directly export static complex heatmaps into an interactive Shiny app. Have a try!
## Citation
Zuguang Gu, et al., [Complex heatmaps reveal patterns and correlations in multidimensional genomic data](http://bioinformatics.oxfordjournals.org/content/early/2016/05/20/bioinformatics.btw313.abstract), Bioinformatics, 2016.
Zuguang Gu. [Complex Heatmap Visualization](https://doi.org/10.1002/imt2.43), iMeta, 2022.
## 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:
- [Make 3D heatmap](https://jokergoo.github.io/2021/03/24/3d-heatmap/)
- [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
### Correlations between methylation, expression and other genomic features
### Visualize Cell Heterogeneity from Single Cell RNASeq
### Making Enhanced OncoPrint
### UpSet plot
<img src="https://user-images.githubusercontent.com/449218/102615477-48c76a80-4136-11eb-98d9-3c528844fbe8.png" width=500 />
### 3D heatmap
## License
MIT @ Zuguang Gu
