<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://travis-ci.org/jokergoo/ComplexHeatmap)
[](https://codecov.io/github/jokergoo/ComplexHeatmap)
[](https://bioconductor.org/packages/stats/bioc/ComplexHeatmap/)
[](https://bioconductor.org/packages/stats/bioc/ComplexHeatmap/)
[](http://bioconductor.org/packages/devel/bioc/html/ComplexHeatmap.html)
## 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
#### Correlations between methylation, expression and other genomic features
#### Visualize Cell Heterogeneity from Single Cell RNASeq
#### Making Enhanced OncoPrint
#### UpSet plot
### License
MIT @ Zuguang Gu
