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This is the development version of ComplexHeatmap; for the stable release version, see ComplexHeatmap.

Make Complex Heatmaps

Bioconductor version: Development (3.20)

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.

Author: Zuguang Gu [aut, cre]

Maintainer: Zuguang Gu < at>

Citation (from within R, enter citation("ComplexHeatmap")):


To install this package, start R (version "4.4") and enter:

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

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

complex_heatmap.html HTML
Most probably asked questions HTML R Script
Reference Manual PDF


biocViews Sequencing, Software, Visualization
Version 2.21.0
In Bioconductor since BioC 3.1 (R-3.2) (9 years)
License MIT + file LICENSE
Depends R (>= 3.5.0), methods, grid, graphics, stats, grDevices
Imports circlize (>= 0.4.14), GetoptLong, colorspace, clue, RColorBrewer, GlobalOptions (>= 0.1.0), png, digest, IRanges, matrixStats, foreach, doParallel, codetools
System Requirements
See More
Suggests testthat (>= 1.0.0), knitr, markdown, dendsort, jpeg, tiff, fastcluster, EnrichedHeatmap, dendextend (>= 1.0.1), grImport, grImport2, glue, GenomicRanges, gridtext, pheatmap (>= 1.0.12), gridGraphics, gplots, rmarkdown, Cairo, magick
Linking To
Depends On Me AMARETTO, EnrichedHeatmap, InteractiveComplexHeatmap, multistateQTL, recoup, sechm, countToFPKM
Imports Me airpart, ASURAT, bettr, BindingSiteFinder, BioNERO, blacksheepr, BloodGen3Module, CATALYST, CCPlotR, celda, CeTF, ClustAll, COCOA, cola, COTAN, CRISPRball, CTexploreR, cytoKernel, dar, DEGreport, DEP, diffcyt, diffUTR, dinoR, ELMER, epiregulon.extra, fCCAC, FLAMES, gCrisprTools, GeDi, GeneTonic, GenomicPlot, GenomicSuperSignature, gmoviz, GRaNIE, hermes, hoodscanR, HybridExpress, InterCellar, iSEE, MAPFX, MatrixQCvis, MesKit, microbiomeMarker, MOMA, monaLisa, Moonlight2R, MultiRNAflow, muscat, musicatk, MWASTools, nipalsMCIA, pathlinkR, PathoStat, PeacoQC, pipeComp, POMA, profileplyr, scRNAseqApp, segmenter, simona, simplifyEnrichment, singleCellTK, TBSignatureProfiler, Xeva, YAPSA, TCGAWorkflow, autoGO, bulkAnalyseR, coda4microbiome, conos, GSSTDA, inferCSN, karyotapR, mineSweepR, missoNet, MitoHEAR, MKomics, ogrdbstats, pkgndep, rKOMICS, rliger, RNAseqQC, RVA, scITD, sigQC, tidyHeatmap, TOmicsVis, visxhclust, wilson
Suggests Me artMS, bambu, clustifyr, CNVRanger, demuxSNP, dittoSeq, EnrichmentBrowser, gtrellis, HilbertCurve, mastR, msImpute, pareg, plotgardener, projectR, QFeatures, raer, scDblFinder, SPIAT, TCGAbiolinks, TCGAutils, weitrix, curatedPCaData, NanoporeRNASeq, BeeBDC, CIARA, circlize, eclust, ggpicrust2, ggsector, grandR, IOHanalyzer, MOSS, multipanelfigure, scCustomize, SCpubr, singleCellHaystack, SpatialDDLS, spiralize, tinyarray
Links To Me
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package ComplexHeatmap_2.21.0.tar.gz
Windows Binary (64-bit only)
macOS Binary (x86_64) ComplexHeatmap_2.21.0.tgz
macOS Binary (arm64) ComplexHeatmap_2.21.0.tgz
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Source Repository (Developer Access) git clone
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