About | ComplexHeatmap Complete Reference (original) (raw)

This is the documentation of theComplexHeatmap package. Examples in the book are generated under version 2.13.1.

You can get a stable Bioconductor version fromhttp://bioconductor.org/packages/release/bioc/html/ComplexHeatmap.html, but the most up-to-date version is always on Github and you can install it by:

The development branch on Bioconductor is basically synchronized to the Github repository.

The ComplexHeatmap package is inspired by the pheatmap package. You can find many arguments in ComplexHeatmap have the same names as in pheatmap. Also you can find this old package that I tried to develop by modifying pheatmap.

Please note, this documentation is not completely compatible with older versions (< 1.99.0, before Oct, 2018), but the major functionality keeps the same.

If you use ComplexHeatmap in your publications, I am appreciated if you can cite any of these two papers:

Gu, Z. (2016) Complex heatmaps reveal patterns and correlations in multidimensional genomic data. Bioinformatics. DOI: 10.1093/bioinformatics/btw313.

Gu, Z. (2022) Complex Heatmap Visualization, iMeta. DOI: 10.1002/imt2.43.

Session info:

## R version 4.2.0 (2022-04-22)
## Platform: x86_64-apple-darwin17.0 (64-bit)
## Running under: macOS Big Sur/Monterey 10.16
## 
## Matrix products: default
## BLAS:   /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib
## 
## locale:
## [1] C/UTF-8/C/C/C/C
## 
## attached base packages:
## [1] grid      stats     graphics  grDevices utils     datasets  methods  
## [8] base     
## 
## other attached packages:
## [1] dendsort_0.3.4        dendextend_1.15.2     circlize_0.4.16      
## [4] ComplexHeatmap_2.13.1 colorout_1.2-2       
## 
## loaded via a namespace (and not attached):
##  [1] png_0.1-7           assertthat_0.2.1    digest_0.6.29      
##  [4] foreach_1.5.2       utf8_1.2.2          R6_2.5.1           
##  [7] stats4_4.2.0        evaluate_0.15       ggplot2_3.3.6      
## [10] pillar_1.7.0        GlobalOptions_0.1.2 rlang_1.0.2        
## [13] jquerylib_0.1.4     S4Vectors_0.34.0    GetoptLong_1.0.5   
## [16] rmarkdown_2.14      stringr_1.4.0       munsell_0.5.0      
## [19] compiler_4.2.0      xfun_0.31           pkgconfig_2.0.3    
## [22] BiocGenerics_0.42.0 shape_1.4.6         htmltools_0.5.2    
## [25] downlit_0.4.0       tidyselect_1.1.2    tibble_3.1.7       
## [28] gridExtra_2.3       bookdown_0.27       IRanges_2.30.0     
## [31] codetools_0.2-18    matrixStats_0.62.0  fansi_1.0.3        
## [34] viridisLite_0.4.0   crayon_1.5.1        dplyr_1.0.9        
## [37] jsonlite_1.8.0      gtable_0.3.0        lifecycle_1.0.1    
## [40] DBI_1.1.2           magrittr_2.0.3      scales_1.2.0       
## [43] stringi_1.7.6       cli_3.3.0           cachem_1.0.6       
## [46] viridis_0.6.2       fs_1.5.2            doParallel_1.0.17  
## [49] xml2_1.3.3          bslib_0.3.1         ellipsis_0.3.2     
## [52] generics_0.1.2      vctrs_0.4.1         rjson_0.2.21       
## [55] RColorBrewer_1.1-3  iterators_1.0.14    tools_4.2.0        
## [58] glue_1.6.2          purrr_0.3.4         parallel_4.2.0     
## [61] fastmap_1.1.0       yaml_2.3.5          clue_0.3-61        
## [64] colorspace_2.0-3    cluster_2.1.3       memoise_2.0.1      
## [67] knitr_1.39          sass_0.4.1

"ComplexHeatmap Complete Reference" was written by Zuguang Gu. It was last built on last revised on 2022-07-31.

This book was built by the bookdown R package.