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00_S4_generic_methods.R 100755 3 kb
00_size.R 100644 9 kb
AdditiveUnit-class.R 100755 4 kb
AnnotationFunction-class.R 100755 14 kb
AnnotationFunction-function.R 100644 123 kb
ColorMapping-class.R 100755 11 kb
Heatmap-class.R 100755 68 kb
Heatmap-draw_component.R 100644 21 kb
Heatmap-layout.R 100644 31 kb
Heatmap-utils.R 100644 7 kb
HeatmapAnnotation-class.R 100755 42 kb
HeatmapList-class.R 100755 29 kb
HeatmapList-draw_component.R 100644 39 kb
HeatmapList-get_order.R 100755 9 kb
HeatmapList-layout.R 100644 62 kb
HeatmapList-legends.R 100644 21 kb
SingleAnnotation-class.R 100755 30 kb
Upset.R 100644 46 kb
annotation_axis.R 100644 11 kb
box_align.R 100644 10 kb
decorate.R 100755 10 kb
densityHeatmap.R 100755 11 kb
global.R 100755 6 kb
grid.Legend.R 100644 39 kb
grid.dendrogram.R 100644 17 kb
gridtext.R 100644 6 kb
is_abs_unit.R 100755 2 kb
oncoPrint.R 100755 29 kb
overview.R 100755 1 kb
stacked_plot.R 100644 0 kb
temp.R 100644 0 kb
utils.R 100755 29 kb
zzz.R 100644 1 kb
README.md
# 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) [![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="600"> 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/ and the website is at https://jokergoo.github.io/ComplexHeatmap. ## 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) ## License MIT @ Zuguang Gu