About
This is the documentation of the ComplexHeatmap package. Examples in the book are generated under version 2.13.1.
You can get a stable Bioconductor version from http://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:
library(devtools)
install_github("jokergoo/ComplexHeatmap")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