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https://github.com/jokergoo/complexheatmap

Make Complex Heatmaps
https://github.com/jokergoo/complexheatmap

clustering complex-heatmaps heatmap

Last synced: 3 days ago
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Make Complex Heatmaps

Host: GitHub
URL: https://github.com/jokergoo/complexheatmap
Owner: jokergoo
License: other
Created: 2015-01-29T11:45:58.000Z (almost 10 years ago)
Default Branch: master
Last Pushed: 2024-09-24T12:48:13.000Z (3 months ago)
Last Synced: 2024-12-19T09:04:24.715Z (3 days ago)
Topics: clustering, complex-heatmaps, heatmap
Language: R
Homepage: https://jokergoo.github.io/ComplexHeatmap-reference/book/
Size: 15.2 MB
Stars: 1,323
Watchers: 35
Forks: 228
Open Issues: 208
Metadata Files:
- Readme: README.md
- Changelog: NEWS
- License: LICENSE
- Code of conduct: CODE_OF_CONDUCT.md

Awesome Lists containing this project

README

        # Make Complex Heatmaps 

[![R-CMD-check](https://github.com/jokergoo/ComplexHeatmap/workflows/R-CMD-check/badge.svg)](https://github.com/jokergoo/ComplexHeatmap/actions)

[![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)



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

![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



### 3D heatmap

![image](https://user-images.githubusercontent.com/449218/112284448-8c77c600-8c89-11eb-8d38-c5538900df20.png)

## License

MIT @ Zuguang Gu