Name Mode Size
..
00_S4_generic_methods.R 100755 3 kb
00_size.R 100644 9 kb
3d.R 100644 4 kb
AdditiveUnit-class.R 100755 4 kb
AnnotationFunction-class.R 100755 15 kb
AnnotationFunction-function.R 100644 151 kb
ColorMapping-class.R 100755 13 kb
Heatmap-class.R 100755 75 kb
Heatmap-draw_component.R 100644 25 kb
Heatmap-layout.R 100644 31 kb
Heatmap-utils.R 100644 9 kb
HeatmapAnnotation-class.R 100755 47 kb
HeatmapList-class.R 100755 61 kb
HeatmapList-draw_component.R 100644 41 kb
HeatmapList-get_order.R 100755 11 kb
HeatmapList-layout.R 100644 66 kb
HeatmapList-legends.R 100644 45 kb
SingleAnnotation-class.R 100755 33 kb
Upset.R 100644 51 kb
anno_textbox.R 100644 14 kb
annotation_axis.R 100644 11 kb
box_align.R 100644 10 kb
decorate.R 100755 10 kb
densityHeatmap.R 100755 17 kb
genomic.R 100644 11 kb
global.R 100755 7 kb
grid.Legend.R 100644 48 kb
grid.dendrogram.R 100644 29 kb
gridtext.R 100644 6 kb
is_abs_unit.R 100755 2 kb
oncoPrint.R 100755 32 kb
other_translation.R 100644 30 kb
overview.R 100755 1 kb
pheatmap_translate.R 100644 20 kb
stacked_plot.R 100644 0 kb
temp.R 100644 0 kb
utils.R 100755 33 kb
zzz.R 100644 2 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> [![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) <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 ![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 <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