@@ -17,7 +17,9 @@ The [**InteractiveComplexHeatmap**](https://github.com/jokergoo/InteractiveCompl

 ## 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, 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

@@ -1,6 +1,6 @@

 # 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) 

+[![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)

@@ -17,7 +17,7 @@ The [**InteractiveComplexHeatmap**](https://github.com/jokergoo/InteractiveCompl

 ## 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

+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

 ## Install

@@ -73,6 +73,7 @@ The full documentations are available at https://jokergoo.github.io/ComplexHeatm

 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/)

@@ -105,6 +105,12 @@ There are following blog posts focusing on specific topics:

 <img src="https://user-images.githubusercontent.com/449218/102615477-48c76a80-4136-11eb-98d9-3c528844fbe8.png" width=500 />

+### 3D heatmap

+

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

+

+

+

 ## License

 MIT @ Zuguang Gu

@@ -13,6 +13,8 @@ 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, 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

@@ -101,7 +101,7 @@ There are following blog posts focusing on specific topics:

 ### UpSet plot

-<img src="https://user-images.githubusercontent.com/449218/102615477-48c76a80-4136-11eb-98d9-3c528844fbe8.png" width=700 />

+<img src="https://user-images.githubusercontent.com/449218/102615477-48c76a80-4136-11eb-98d9-3c528844fbe8.png" width=500 />

 ## License

@@ -101,14 +101,7 @@ There are following blog posts focusing on specific topics:

 ### 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" />

-

+<img src="https://user-images.githubusercontent.com/449218/102615477-48c76a80-4136-11eb-98d9-3c528844fbe8.png" width=700 />

 ## License

@@ -107,7 +107,7 @@ There are following blog posts focusing on specific topics:

 Heatmaps can be exported into a Shiny app by `ht_shiny(ht)`. See examples at https://jokergoo.shinyapps.io/interactive_complexheatmap/.

-https://user-images.githubusercontent.com/449218/82199376-e5eec600-98fd-11ea-9fca-ad95d405dc20.gif

+<img src="https://user-images.githubusercontent.com/449218/82199376-e5eec600-98fd-11ea-9fca-ad95d405dc20.gif" />

 ## License

@@ -71,14 +71,14 @@ The full documentations are available at https://jokergoo.github.io/ComplexHeatm

 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/)

+- [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

@@ -17,9 +17,6 @@ heatmaps and supports various annotation graphics.

 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/ and the website is at https://jokergoo.github.io/ComplexHeatmap.

 ## Install

@@ -66,6 +63,24 @@ 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

@@ -88,6 +103,13 @@ Heatmap(mat1, ...) + Heatmap(mat2, ...) + ha

 ![](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/.

+

+https://user-images.githubusercontent.com/449218/82199376-e5eec600-98fd-11ea-9fca-ad95d405dc20.gif

+

+

 ## License

 MIT @ Zuguang Gu

@@ -3,7 +3,6 @@

 [![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://mcube.nju.edu.cn/cgi-bin/zuguanggu/bioc_download.pl?package=ComplexHeatmap&)](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">

@@ -6,7 +6,7 @@

 [![bioc](http://mcube.nju.edu.cn/cgi-bin/zuguanggu/bioc_download.pl?package=ComplexHeatmap&)](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="600">

+<img src="http://jokergoo.github.io/complexheatmap_logo.svg" width="550">

 Complex heatmaps are efficient to visualize associations between different

@@ -1,4 +1,4 @@

-<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>

+# 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) 

@@ -8,26 +8,25 @@

 <img src="http://jokergoo.github.io/complexheatmap_logo.svg" width="600">

-## 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

+## 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

+## Documentation

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

+The full documentations are available at https://jokergoo.github.io/ComplexHeatmap-reference/book/ and the website is at https://jokergoo.github.io/ComplexHeatmap.

-### Install

+## Install

 `ComplexHeatmap` is available on [Bioconductor](http://www.bioconductor.org/packages/devel/bioc/html/ComplexHeatmap.html), you can install it by:

-```{r}

+```r

 if (!requireNamespace("BiocManager", quietly=TRUE))

     install.packages("BiocManager")

 BiocManager::install("ComplexHeatmap")

@@ -35,62 +34,62 @@ BiocManager::install("ComplexHeatmap")

 If you want the latest version, install it directly from GitHub:

-```{r}

+```r

 library(devtools)

 install_github("jokergoo/ComplexHeatmap")

 ```

-### Usage

+## Usage

 Make a single heatmap:

-```{r}

+```r

 Heatmap(mat, ...)

 ```

 A single Heatmap with column annotations:

-```{r}

+```r

 ha = HeatmapAnnotation(df = anno1, anno_fun = anno2, ...)

 Heatmap(mat, ..., top_annotation = ha)

 ```

 Make a list of heatmaps:

-```{r}

+```r

 Heatmap(mat1, ...) + Heatmap(mat2, ...)

 ```

 Make a list of heatmaps and row annotations:

-```{r}

+```r

 ha = HeatmapAnnotation(df = anno1, anno_fun = anno2, ..., which = "row")

 Heatmap(mat1, ...) + Heatmap(mat2, ...) + ha

 ```

-### Examples

+## Examples

-#### Visualize Methylation Profile with Complex Annotations

+### 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

+### 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

+### 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

+### Making Enhanced OncoPrint

 ![complexheatmap_example1](https://user-images.githubusercontent.com/449218/47718638-2ec22980-dc49-11e8-845e-21e51d3b8e73.png)

-#### UpSet plot

+### UpSet plot

-![](https://pbs.twimg.com/media/Dvpp31uX4AAqGDP.jpg:large)

+![](https://pbs.twimg.com/media/Dvpp31uX4AAqGDP.jpg)

-### License

+## License

 MIT @ Zuguang Gu

@@ -6,6 +6,8 @@

 [![bioc](http://mcube.nju.edu.cn/cgi-bin/zuguanggu/bioc_download.pl?package=ComplexHeatmap&)](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="600">

+

 ## Make Complex Heatmaps

 Complex heatmaps are efficient to visualize associations between different

@@ -2,7 +2,7 @@

 [![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/ComplexHeatmap.svg)](https://bioconductor.org/packages/stats/bioc/ComplexHeatmap/) 

+[![bioc](http://www.bioconductor.org/shields/downloads/devel/ComplexHeatmap.svg)](https://bioconductor.org/packages/stats/bioc/ComplexHeatmap/) 

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

@@ -84,6 +84,10 @@ Heatmap(mat1, ...) + Heatmap(mat2, ...) + ha

 ![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

@@ -23,7 +23,7 @@ The full documentations are available at https://jokergoo.github.io/ComplexHeatm

 ### Install

-`ComplexHeatmap` is available on [Bioconductor](http://www.bioconductor.org/packages/devel/bioc/html/ComplexHeatmap.html), you can intall it by:

+`ComplexHeatmap` is available on [Bioconductor](http://www.bioconductor.org/packages/devel/bioc/html/ComplexHeatmap.html), you can install it by:

 ```{r}

 source("http://bioconductor.org/biocLite.R")

@@ -1,3 +1,5 @@

+<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/ComplexHeatmap.svg)](https://bioconductor.org/packages/stats/bioc/ComplexHeatmap/) 

@@ -6,40 +8,18 @@

 ## Make Complex Heatmaps

-Complex heatmaps are efficient to visualize associations 

-between different sources of data sets and reveal potential structures. 

-Here the **ComplexHeatmap** package provides a highly flexible way to arrange 

-multiple heatmaps and supports self-defined annotation graphics.

+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

-### General design

-

-Generally, a heatmap list contains several heatmaps and row annotations.

-

-![default](https://cloud.githubusercontent.com/assets/449218/6541828/75c77f8a-c4e5-11e4-80af-6ebb5e649898.png)

-

-Surrounding the heatmap list,

-there are legends for heatmaps and annotations, also there are titles which are placed

-on the four sides of the heatmap list. And for each heatmap, there are also different components

-surrounding the heatmap body.

-

-The **ComplexHeatmap** package is implemented in an object-oriented way. To describe a heatmap list, 

-there are following classes:

-

-- `Heatmap` class: a single heatmap containing heatmap body, row/column names, titles, dendrograms and column annotations.

-- `HeatmapList` class: a list of heatmaps and row annotations.

-- `HeatmapAnnotation` class: defines a list of row annotations and column annotations.

-

-There are also several internal classes:

-

-- `SingleAnnotation` class: defines a single row annotation or column annotation.

-- `ColorMapping` class: mapping from values to colors.

+### Documentation

-**ComplexHeatmap** is implemented under **grid** system, so users should know basic **grid** functionality

-to get full use of the package.

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

 ### Install

@@ -85,108 +65,25 @@ ha = HeatmapAnnotation(df = anno1, anno_fun = anno2, ..., which = "row")

 Heatmap(mat1, ...) + Heatmap(mat2, ...) + ha

 ```

-### As a base package

-

-**ComplexHeatmap** can be used as a base package to build other packages which focus

-On specific applications. E.g. [EnrichedHeatmap](http://github.com/jokergoo/EnrichedHeatmap) package

-uses **ComplexHeatmap** as base to make heatmaps which visualize the enrichment of genomic signals

-to specific target regions.

-

-### Vignettes

-

-There are several vignettes in the package. Each vignette focuses on a specific topic. Following

-lists the general topics discussed in these vignettes:

-

-  1. [**Making a Single Heatmap**](http://www.bioconductor.org/packages/devel/bioc/vignettes/ComplexHeatmap/inst/doc/s2.single_heatmap.html)

-

-    This vignette introduces the basic configuration for making a single heatmap. Similar as other

-    R functions/packages, the basic usage is quite similar, but there are several unique features

-    for **ComplexHeamtap** package.

-    - Works both for numeric matrix and character matrix

-    - For numeric matrix which contains continuous values, the package allows a color mapping function

-      which can give more accurate colors and be robust to outliers.

-    - Highly flexible for clustering. You can define the distance method for clustering by:

-          * a pre-defined distance such as "euclidean" or "pearson"

-          * a self-defined function which calculates distance from a matrix.

-          * a self-defined function which calculates distance from two vectors

-        

-        You can define the clustering method by:

-          * a clustering function such as `diana()` from **cluster** package

-          * a `hclust` or `dendrogram` object.

-    - `NA` is allowed for clustering and heatmap visualization.

-    - Dendrogram and dimension names can be put on any side of the heatmap.

-    - Rows on the heatmap can be split by `cutree`, by `kmeans` or by a data frame which contains 

-      different levels that split the heatmap.

-    - The heatmap body itself can be completely self-defined.

-

-  2. [**Making a List of Heatmaps**](http://www.bioconductor.org/packages/devel/bioc/vignettes/ComplexHeatmap/inst/doc/s3.a_list_of_heatmaps.html)

-

-    This vignette introduces how to concatenate a list of heatmaps and how adjustment is applied to keep

-    the correspondence of the heatmaps.

+### Examples

-  3. [**Heatmap Annotations**](http://www.bioconductor.org/packages/devel/bioc/vignettes/ComplexHeatmap/inst/doc/s4.heatmap_annotation.html)

+#### Visualize Methylation Profile with Complex Annotations

-    This vignette introduces the concept of the heatmap annotation and demonstrate how to make simple annotations

-    as well as complex annotations. Also, the vignette explains the difference between column annotations

-    and row annotations.

+![complexheatmap_example4](https://user-images.githubusercontent.com/449218/47718635-2ec22980-dc49-11e8-9f01-37becb19e0d5.png)

-  4. [**Heatmap and Annotation Legends**](http://www.bioconductor.org/packages/devel/bioc/vignettes/ComplexHeatmap/inst/doc/s5.legend.html)

+#### Correlations between methylation, expression and other genomic features

-    This vignette introduces how to configurate the heatmap legend and annotation legend, also

-    how to add self-defined legends.

+![complexheatmap_example3](https://user-images.githubusercontent.com/449218/47718636-2ec22980-dc49-11e8-8db0-1659c27dcf40.png)

-  5. [**Heatmap Decoration**](http://www.bioconductor.org/packages/devel/bioc/vignettes/ComplexHeatmap/inst/doc/s6.heatmap_decoration.html)

+#### Visualize Cell Heterogeneity from Single Cell RNASeq

-    This vignette introduces methods to add more self-defined graphics to the heatmaps after the heatmaps

-    are generated.

+![complexheatmap_example2](https://user-images.githubusercontent.com/449218/47718637-2ec22980-dc49-11e8-925e-955c16cfa982.png)

-  6. [**Interactive with Heatmaps**](http://www.bioconductor.org/packages/devel/bioc/vignettes/ComplexHeatmap/inst/doc/s7.interactive.html)

+#### Making Enhanced OncoPrint

-    How to select a region in the heatmap to retrieve the sub-matrix.

-  

-  7. [**OncoPrint**](http://www.bioconductor.org/packages/devel/bioc/vignettes/ComplexHeatmap/inst/doc/s8.oncoprint.html)

-

-    How to make an oncoPrint.

-

-  8. [**Examples**](http://www.bioconductor.org/packages/devel/bioc/vignettes/ComplexHeatmap/inst/doc/s9.examples.html)

-

-    More simulated and real-world examples are shown in this vignette.

-    

-

-### Visualize high dimensional genomic data

-

-The examples visualizes correlation between methylation and expression, as well as other annotation information (data are randomly generated). In the heatmap, each row corresponds to a differentially methylated regions (DMRs). 

-From left to right, heatmaps are:

-

-1. methylation for each DMRs in samples.

-2. direction of the methylation (one column heatmap), i.e. is methylation hyper in tumor or hypo?

-3. expression for the genes that are associated with corresponding DMRs (e.g. closest gene).

-4. signiciance for the correlation between methylation and expression (-log10(p-value)).

-5. type of genes, i.e. is the gene a protein coding gene or a lincRNA?

-6. annotation to gene models, i.e. is the DMR located in the intragenic region of the corresponding gene or the DMR is intergenic?

-7. distance from the DMR to the TSS of the corresponding gene.

-8. overlapping between DMRs and enhancers (Color shows how much the DMR is covered by the enhancers).

-

-![download](https://cloud.githubusercontent.com/assets/449218/9685180/dddf30c0-531c-11e5-805a-4cc5a36e9197.png)

-

-### OncoPrint

-

-<a href="http://www.cbioportal.org/faq.jsp#what-are-oncoprints">OncoPrint</a> visualize multiple genomic alteration

-events through a heatmap. From verion 1.3.0, **ComplexHeatmap** package provides a new `oncoPrint()` function. By this

-function, users can define their own graphics which correspond to differnet alteration events. Also the function additionally

-add barplots on two sides of the heatmap which tell number of different alterations in patients or samples.

-

-With general functionality of **ComplexHeamtap**, you can add more heatmaps / row annotations to the oncoPrint, even split the

-oncoPrint to enphasize sub groups.

-

-![oncoprint](https://cloud.githubusercontent.com/assets/449218/9370313/9c9b6b00-46cf-11e5-9740-c5c2a7a40eb5.png)

-

-### Interact with heatmaps

-

-You can use mouse to select a region on the heatmap, it will return row index and column index which correspond to the selected region.

-

-<p><img src="https://cloud.githubusercontent.com/assets/449218/10479344/2981c27a-7264-11e5-9868-7400c5dc620d.gif", width="600"></p>

+![complexheatmap_example1](https://user-images.githubusercontent.com/449218/47718638-2ec22980-dc49-11e8-845e-21e51d3b8e73.png)

 ### License

-GPL (>= 2)

+MIT @ Zuguang Gu

+

@@ -46,8 +46,9 @@ to get full use of the package.

 `ComplexHeatmap` is available on [Bioconductor](http://www.bioconductor.org/packages/devel/bioc/html/ComplexHeatmap.html), you can intall it by:

 ```{r}

-source("http://bioconductor.org/biocLite.R")

-biocLite("ComplexHeatmap")

+if (!requireNamespace("BiocManager", quietly=TRUE))

+    install.packages("BiocManager")

+BiocManager::install("ComplexHeatmap")

 ```

 If you want the latest version, install it directly from GitHub:

@@ -1,7 +1,7 @@

 [![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/ComplexHeatmap.svg)](https://bioconductor.org/packages/stats/bioc/ComplexHeatmap/) 

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

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

 ## Make Complex Heatmaps

@@ -1,4 +1,8 @@

-[![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/ComplexHeatmap.svg)](https://bioconductor.org/packages/stats/bioc/ComplexHeatmap/) ![bioc](http://www.bioconductor.org/shields/years-in-bioc/ComplexHeatmap.svg)

+[![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/ComplexHeatmap.svg)](https://bioconductor.org/packages/stats/bioc/ComplexHeatmap/) 

+[![bioc](http://mcube.nju.edu.cn/cgi-bin/zuguanggu/bioc_download.pl?package=ComplexHeatmap)](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)

 ## Make Complex Heatmaps

@@ -1,4 +1,4 @@

-[![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/ComplexHeatmap.svg)](http://bioconductor.org/packages/stats/bioc/ComplexHeatmap.html) ![bioc](http://www.bioconductor.org/shields/years-in-bioc/ComplexHeatmap.svg)

+[![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/ComplexHeatmap.svg)](https://bioconductor.org/packages/stats/bioc/ComplexHeatmap/) ![bioc](http://www.bioconductor.org/shields/years-in-bioc/ComplexHeatmap.svg)

 ## Make Complex Heatmaps

@@ -7,6 +7,10 @@ between different sources of data sets and reveal potential structures.

 Here the **ComplexHeatmap** package provides a highly flexible way to arrange 

 multiple heatmaps and supports self-defined 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

+

 ### General design

 Generally, a heatmap list contains several heatmaps and row annotations.

@@ -1,14 +1,13 @@

-[![Build Status](https://travis-ci.org/jokergoo/ComplexHeatmap.svg)](https://travis-ci.org/jokergoo/ComplexHeatmap)

+[![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/ComplexHeatmap.svg)](http://bioconductor.org/packages/stats/bioc/ComplexHeatmap.html) ![bioc](http://www.bioconductor.org/shields/years-in-bioc/ComplexHeatmap.svg)

-Make Complex Heatmaps

-=========================

+## Make Complex Heatmaps

 Complex heatmaps are efficient to visualize associations 

 between different sources of data sets and reveal potential structures. 

 Here the **ComplexHeatmap** package provides a highly flexible way to arrange 

 multiple heatmaps and supports self-defined annotation graphics.

-## General design

+### General design

 Generally, a heatmap list contains several heatmaps and row annotations.

@@ -179,3 +178,7 @@ oncoPrint to enphasize sub groups.

 You can use mouse to select a region on the heatmap, it will return row index and column index which correspond to the selected region.

 <p><img src="https://cloud.githubusercontent.com/assets/449218/10479344/2981c27a-7264-11e5-9868-7400c5dc620d.gif", width="600"></p>

+

+### License

+

+GPL (>= 2)

@@ -90,7 +90,7 @@ to specific target regions.

 There are several vignettes in the package. Each vignette focuses on a specific topic. Following

 lists the general topics discussed in these vignettes:

-  1. [**Making a Single Heatmap**](http://http://www.bioconductor.org/packages/devel/bioc/vignettes/ComplexHeatmap/inst/doc/s2.single_heatmap.html)

+  1. [**Making a Single Heatmap**](http://www.bioconductor.org/packages/devel/bioc/vignettes/ComplexHeatmap/inst/doc/s2.single_heatmap.html)

     This vignette introduces the basic configuration for making a single heatmap. Similar as other

     R functions/packages, the basic usage is quite similar, but there are several unique features

@@ -112,36 +112,36 @@ lists the general topics discussed in these vignettes:

       different levels that split the heatmap.

     - The heatmap body itself can be completely self-defined.

-  2. [**Making a List of Heatmaps**](http://http://www.bioconductor.org/packages/devel/bioc/vignettes/ComplexHeatmap/inst/doc/s3.a_list_of_heatmaps.html)

+  2. [**Making a List of Heatmaps**](http://www.bioconductor.org/packages/devel/bioc/vignettes/ComplexHeatmap/inst/doc/s3.a_list_of_heatmaps.html)

     This vignette introduces how to concatenate a list of heatmaps and how adjustment is applied to keep

     the correspondence of the heatmaps.

-  3. [**Heatmap Annotations**](http://http://www.bioconductor.org/packages/devel/bioc/vignettes/ComplexHeatmap/inst/doc/s4.heatmap_annotation.html)

+  3. [**Heatmap Annotations**](http://www.bioconductor.org/packages/devel/bioc/vignettes/ComplexHeatmap/inst/doc/s4.heatmap_annotation.html)

     This vignette introduces the concept of the heatmap annotation and demonstrate how to make simple annotations

     as well as complex annotations. Also, the vignette explains the difference between column annotations

     and row annotations.

-  4. [**Heatmap and Annotation Legends**](http://http://www.bioconductor.org/packages/devel/bioc/vignettes/ComplexHeatmap/inst/doc/s5.legend.html)

+  4. [**Heatmap and Annotation Legends**](http://www.bioconductor.org/packages/devel/bioc/vignettes/ComplexHeatmap/inst/doc/s5.legend.html)

     This vignette introduces how to configurate the heatmap legend and annotation legend, also

     how to add self-defined legends.

-  5. [**Heatmap Decoration**](http://http://www.bioconductor.org/packages/devel/bioc/vignettes/ComplexHeatmap/inst/doc/s6.heatmap_decoration.html)

+  5. [**Heatmap Decoration**](http://www.bioconductor.org/packages/devel/bioc/vignettes/ComplexHeatmap/inst/doc/s6.heatmap_decoration.html)

     This vignette introduces methods to add more self-defined graphics to the heatmaps after the heatmaps

     are generated.

-  6. [**Interactive with Heatmaps**](http://http://www.bioconductor.org/packages/devel/bioc/vignettes/ComplexHeatmap/inst/doc/s7.interactive.html)

+  6. [**Interactive with Heatmaps**](http://www.bioconductor.org/packages/devel/bioc/vignettes/ComplexHeatmap/inst/doc/s7.interactive.html)

     How to select a region in the heatmap to retrieve the sub-matrix.

-  7. [**OncoPrint**](http://http://www.bioconductor.org/packages/devel/bioc/vignettes/ComplexHeatmap/inst/doc/s8.oncoprint.html)

+  7. [**OncoPrint**](http://www.bioconductor.org/packages/devel/bioc/vignettes/ComplexHeatmap/inst/doc/s8.oncoprint.html)

     How to make an oncoPrint.

-  8. [**Examples**](http://http://www.bioconductor.org/packages/devel/bioc/vignettes/ComplexHeatmap/inst/doc/s9.examples.html)

+  8. [**Examples**](http://www.bioconductor.org/packages/devel/bioc/vignettes/ComplexHeatmap/inst/doc/s9.examples.html)

     More simulated and real-world examples are shown in this vignette.

@@ -3,23 +3,40 @@

 Make Complex Heatmaps

 =========================

-Complex heatmaps are efficient to visualize associations between different sources of data sets and reveal potential features. Here the ComplexHeatmap package provides a highly flexible way to arrange multiple heatmaps and supports self-defined annotation graphics.

+Complex heatmaps are efficient to visualize associations 

+between different sources of data sets and reveal potential structures. 

+Here the **ComplexHeatmap** package provides a highly flexible way to arrange 

+multiple heatmaps and supports self-defined annotation graphics.

-A single heatmap or a list of heatmaps are composed by basic components:

+## General design

+

+Generally, a heatmap list contains several heatmaps and row annotations.

 ![default](https://cloud.githubusercontent.com/assets/449218/6541828/75c77f8a-c4e5-11e4-80af-6ebb5e649898.png)

-The package makes heatmaps in an object-oriented way by abstracting heatmaps into several classes:

+Surrounding the heatmap list,

+there are legends for heatmaps and annotations, also there are titles which are placed

+on the four sides of the heatmap list. And for each heatmap, there are also different components

+surrounding the heatmap body.

+

+The **ComplexHeatmap** package is implemented in an object-oriented way. To describe a heatmap list, 

+there are following classes:

+

+- `Heatmap` class: a single heatmap containing heatmap body, row/column names, titles, dendrograms and column annotations.

+- `HeatmapList` class: a list of heatmaps and row annotations.

+- `HeatmapAnnotation` class: defines a list of row annotations and column annotations.

-- `Heatmap` a single heatmap

-- `HeatmapList` a list of heatmaps

-- `HeatmapAnnotation` annotation on columns or rows

+There are also several internal classes:

-and provides methods for arranging and plotting heatmap components.

+- `SingleAnnotation` class: defines a single row annotation or column annotation.

+- `ColorMapping` class: mapping from values to colors.

-## Install

+**ComplexHeatmap** is implemented under **grid** system, so users should know basic **grid** functionality

+to get full use of the package.

-`ComplexHeatmap` is available on Bioconductor, you can intall it by:

+### Install

+

+`ComplexHeatmap` is available on [Bioconductor](http://www.bioconductor.org/packages/devel/bioc/html/ComplexHeatmap.html), you can intall it by:

 ```{r}

 source("http://bioconductor.org/biocLite.R")

@@ -33,7 +50,7 @@ library(devtools)

 install_github("jokergoo/ComplexHeatmap")

 ```

-## Usage

+### Usage

 Make a single heatmap:

@@ -61,14 +78,75 @@ ha = HeatmapAnnotation(df = anno1, anno_fun = anno2, ..., which = "row")

 Heatmap(mat1, ...) + Heatmap(mat2, ...) + ha

 ```

-## As a base package

+### As a base package

 **ComplexHeatmap** can be used as a base package to build other packages which focus

 On specific applications. E.g. [EnrichedHeatmap](http://github.com/jokergoo/EnrichedHeatmap) package

 uses **ComplexHeatmap** as base to make heatmaps which visualize the enrichment of genomic signals

 to specific target regions.

-## Visualize high dimensional genomic data

+### Vignettes

+

+There are several vignettes in the package. Each vignette focuses on a specific topic. Following

+lists the general topics discussed in these vignettes:

+

+  1. [**Making a Single Heatmap**](http://http://www.bioconductor.org/packages/devel/bioc/vignettes/ComplexHeatmap/inst/doc/s2.single_heatmap.html)

+

+    This vignette introduces the basic configuration for making a single heatmap. Similar as other

+    R functions/packages, the basic usage is quite similar, but there are several unique features

+    for **ComplexHeamtap** package.

+    - Works both for numeric matrix and character matrix

+    - For numeric matrix which contains continuous values, the package allows a color mapping function

+      which can give more accurate colors and be robust to outliers.

+    - Highly flexible for clustering. You can define the distance method for clustering by:

+          * a pre-defined distance such as "euclidean" or "pearson"

+          * a self-defined function which calculates distance from a matrix.

+          * a self-defined function which calculates distance from two vectors

+        

+        You can define the clustering method by:

+          * a clustering function such as `diana()` from **cluster** package

+          * a `hclust` or `dendrogram` object.

+    - `NA` is allowed for clustering and heatmap visualization.

+    - Dendrogram and dimension names can be put on any side of the heatmap.

+    - Rows on the heatmap can be split by `cutree`, by `kmeans` or by a data frame which contains 

+      different levels that split the heatmap.

+    - The heatmap body itself can be completely self-defined.

+

+  2. [**Making a List of Heatmaps**](http://http://www.bioconductor.org/packages/devel/bioc/vignettes/ComplexHeatmap/inst/doc/s3.a_list_of_heatmaps.html)

+

+    This vignette introduces how to concatenate a list of heatmaps and how adjustment is applied to keep

+    the correspondence of the heatmaps.

+

+  3. [**Heatmap Annotations**](http://http://www.bioconductor.org/packages/devel/bioc/vignettes/ComplexHeatmap/inst/doc/s4.heatmap_annotation.html)

+

+    This vignette introduces the concept of the heatmap annotation and demonstrate how to make simple annotations

+    as well as complex annotations. Also, the vignette explains the difference between column annotations

+    and row annotations.

+

+  4. [**Heatmap and Annotation Legends**](http://http://www.bioconductor.org/packages/devel/bioc/vignettes/ComplexHeatmap/inst/doc/s5.legend.html)

+

+    This vignette introduces how to configurate the heatmap legend and annotation legend, also

+    how to add self-defined legends.

+

+  5. [**Heatmap Decoration**](http://http://www.bioconductor.org/packages/devel/bioc/vignettes/ComplexHeatmap/inst/doc/s6.heatmap_decoration.html)

+

+    This vignette introduces methods to add more self-defined graphics to the heatmaps after the heatmaps

+    are generated.

+

+  6. [**Interactive with Heatmaps**](http://http://www.bioconductor.org/packages/devel/bioc/vignettes/ComplexHeatmap/inst/doc/s7.interactive.html)

+

+    How to select a region in the heatmap to retrieve the sub-matrix.

+  

+  7. [**OncoPrint**](http://http://www.bioconductor.org/packages/devel/bioc/vignettes/ComplexHeatmap/inst/doc/s8.oncoprint.html)

+

+    How to make an oncoPrint.

+

+  8. [**Examples**](http://http://www.bioconductor.org/packages/devel/bioc/vignettes/ComplexHeatmap/inst/doc/s9.examples.html)

+

+    More simulated and real-world examples are shown in this vignette.

+    

+

+### Visualize high dimensional genomic data

 The examples visualizes correlation between methylation and expression, as well as other annotation information (data are randomly generated). In the heatmap, each row corresponds to a differentially methylated regions (DMRs). 

 From left to right, heatmaps are:

@@ -84,7 +162,7 @@ From left to right, heatmaps are:

 ![download](https://cloud.githubusercontent.com/assets/449218/9685180/dddf30c0-531c-11e5-805a-4cc5a36e9197.png)

-## OncoPrint

+### OncoPrint

 <a href="http://www.cbioportal.org/faq.jsp#what-are-oncoprints">OncoPrint</a> visualize multiple genomic alteration

 events through a heatmap. From verion 1.3.0, **ComplexHeatmap** package provides a new `oncoPrint()` function. By this

@@ -96,8 +174,8 @@ oncoPrint to enphasize sub groups.

 ![oncoprint](https://cloud.githubusercontent.com/assets/449218/9370313/9c9b6b00-46cf-11e5-9740-c5c2a7a40eb5.png)

-## Interact with heatmaps

+### Interact with heatmaps

 You can use mouse to select a region on the heatmap, it will return row index and column index which correspond to the selected region.

-![select_region](https://cloud.githubusercontent.com/assets/449218/10479344/2981c27a-7264-11e5-9868-7400c5dc620d.gif)

+<p><img src="https://cloud.githubusercontent.com/assets/449218/10479344/2981c27a-7264-11e5-9868-7400c5dc620d.gif", width="600"></p>

@@ -100,4 +100,4 @@ oncoPrint to enphasize sub groups.

 You can use mouse to select a region on the heatmap, it will return row index and column index which correspond to the selected region.

-![download](https://cloud.githubusercontent.com/assets/449218/9685087/456d6276-531c-11e5-9837-2ba8a081ad50.gif)

+![select_region](https://cloud.githubusercontent.com/assets/449218/10479344/2981c27a-7264-11e5-9868-7400c5dc620d.gif)

old mode 100644

new mode 100755

@@ -82,7 +82,7 @@ From left to right, heatmaps are:

 7. distance from the DMR to the TSS of the corresponding gene.

 8. overlapping between DMRs and enhancers (Color shows how much the DMR is covered by the enhancers).

-![example](https://cloud.githubusercontent.com/assets/449218/6862097/1bc46436-d443-11e4-91f5-431bc9210c80.png)

+![download](https://cloud.githubusercontent.com/assets/449218/9685180/dddf30c0-531c-11e5-805a-4cc5a36e9197.png)

 ## OncoPrint

@@ -95,3 +95,9 @@ With general functionality of **ComplexHeamtap**, you can add more heatmaps / ro

 oncoPrint to enphasize sub groups.

 ![oncoprint](https://cloud.githubusercontent.com/assets/449218/9370313/9c9b6b00-46cf-11e5-9740-c5c2a7a40eb5.png)

+

+## Interact with heatmaps

+

+You can use mouse to select a region on the heatmap, it will return row index and column index which correspond to the selected region.

+

+![download](https://cloud.githubusercontent.com/assets/449218/9685087/456d6276-531c-11e5-9837-2ba8a081ad50.gif)