Package: ComplexHeatmap 2.23.0

Zuguang Gu

ComplexHeatmap: Make Complex Heatmaps

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.

Authors:Zuguang Gu [aut, cre]

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NEWS

# Install 'ComplexHeatmap' in R:
install.packages('ComplexHeatmap', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/jokergoo/complexheatmap/issues

On BioConductor:ComplexHeatmap-2.23.0(bioc 3.21)ComplexHeatmap-2.22.0(bioc 3.20)

softwarevisualizationsequencingclusteringcomplex-heatmapsheatmap

16.88 score 1.3k stars 147 packages 14k scripts 25k downloads 565 mentions 210 exports 21 dependencies

Last updated 1 months agofrom:29bc18500a. Checks:OK: 3 NOTE: 4. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 29 2024
R-4.5-winNOTENov 29 2024
R-4.5-linuxNOTENov 29 2024
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R-4.3-winOKNov 29 2024
R-4.3-macOKNov 29 2024

Exports:[.AnnotationFunction[.comb_mat[.gridtext[.Heatmap[.HeatmapAnnotation[.HeatmapList[.SingleAnnotation%v%+.AdditiveUnitadd_heatmapAdditiveUnitadjust_dend_by_xadjust_heatmap_listalter_graphicanno_barplotanno_blockanno_boxplotanno_customizeanno_densityanno_emptyanno_histogramanno_horizonanno_imageanno_joyplotanno_linesanno_linkanno_markanno_numericanno_oncoprint_barplotanno_pointsanno_simpleanno_summaryanno_textanno_textboxanno_zoomannotation_axis_grobannotation_legend_sizeAnnotationFunctionattach_annotationbar3Dbin_genomec.ColorMappingc.HeatmapAnnotationcluster_between_groupscluster_within_groupcolor_mapping_legendColorMappingcolumn_dendcolumn_ordercolumnAnnotationcomb_degreecomb_namecomb_sizecompare_heatmapcompare_heatmap.2compare_pheatmapcomplement_sizecomponent_heightcomponent_widthcopy_alldecorate_annotationdecorate_column_denddecorate_column_namesdecorate_column_titledecorate_denddecorate_dimnamesdecorate_heatmap_bodydecorate_row_denddecorate_row_namesdecorate_row_titledecorate_titledefault_axis_paramdefault_get_typedend_heightsdend_xydendrogramGrobdensityHeatmapdim.Heatmapdist2drawdraw_annotationdraw_annotation_legenddraw_denddraw_dimnamesdraw_heatmap_bodydraw_heatmap_legenddraw_heatmap_listdraw_titleextract_combfrequencyHeatmapfull_comb_codeget_color_mapping_listget_legend_param_listgetXY_in_parent_vpgrid.annotation_axisgrid.boxplotgrid.dendrogramgrid.draw.Legendsgrid.textboxgt_renderHeatmapheatmap_legend_sizeHeatmap3DHeatmapAnnotationHeatmapListheight.AnnotationFunctionheight.Heatmapheight.HeatmapAnnotationheight.HeatmapListheight.Legendsheight.SingleAnnotationheight<-.AnnotationFunctionheight<-.HeatmapAnnotationheight<-.SingleAnnotationheightDetails.annotation_axisheightDetails.legendheightDetails.legend_bodyheightDetails.packed_legendsheightDetails.textboxht_global_optht_optht_sizeis_abs_unitLegendLegendslength.HeatmapAnnotationlength.HeatmapListlist_componentslist_to_matrixmake_column_clustermake_comb_matmake_layoutmake_row_clustermap_to_colorsmax_text_heightmax_text_widthmerge_dendrogramnames.HeatmapAnnotationnames.HeatmapListnames<-.HeatmapAnnotationncol.Heatmapnobs.AnnotationFunctionnobs.HeatmapAnnotationnobs.SingleAnnotationnormalize_comb_matnormalize_genomic_signals_to_binsnrow.HeatmaponcoPrintorder.comb_matpackLegendpheatmappindexplot.Heatmapplot.HeatmapAnnotationplot.HeatmapListprepareprint.comb_matre_sizerestore_matrixrow_anno_barplotrow_anno_boxplotrow_anno_densityrow_anno_histogramrow_anno_pointsrow_anno_textrow_dendrow_orderrowAnnotationset_component_heightset_component_widthset_nameset_name<-set_sizeSingleAnnotationsize.AnnotationFunctionsize.HeatmapAnnotationsize.SingleAnnotationsize<-.AnnotationFunctionsize<-.HeatmapAnnotationsize<-.SingleAnnotationsmartAlign2str.comb_matsubset_gpsubset_matrix_by_rowsubset_nosubset_vectorsummary.Heatmapsummary.HeatmapListt.comb_mattest_alter_funtextbox_grobunify_mat_listUpSetupset_left_annotationupset_right_annotationupset_top_annotationwidth.AnnotationFunctionwidth.Heatmapwidth.HeatmapAnnotationwidth.HeatmapListwidth.Legendswidth.SingleAnnotationwidth<-.AnnotationFunctionwidth<-.HeatmapAnnotationwidth<-.SingleAnnotationwidthDetails.annotation_axiswidthDetails.legendwidthDetails.legend_bodywidthDetails.packed_legendswidthDetails.textbox

Dependencies:BiocGenericscirclizeclueclustercodetoolscolorspacecrayondigestdoParallelforeachgenericsGetoptLongGlobalOptionsIRangesiteratorsmatrixStatspngRColorBrewerrjsonS4Vectorsshape

ComplexHeatmap vignette

Rendered fromcomplex_heatmap.rmdusingknitron Nov 29 2024.

Last update: 2021-02-12
Started: 2018-10-23

Most probably asked questions

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Last update: 2021-02-09
Started: 2018-10-30

Readme and manuals

Help Manual

Help pageTopics
Make complex heatmapsComplexHeatmap-package
Subset an AnnotationFunction ObjectExtract.AnnotationFunction [.AnnotationFunction
Subset the Combination MatrixExtract.comb_mat [.comb_mat
Subset method of gridtext classExtract.gridtext [.gridtext
Subset a HeatmapExtract.Heatmap [.Heatmap
Subset the HeatmapAnnotation objectExtract.HeatmapAnnotation [.HeatmapAnnotation
Subset a HeatmapList objectExtract.HeatmapList [.HeatmapList
Subset an SingleAnnotation ObjectExtract.SingleAnnotation [.SingleAnnotation
Vertically Add Heatmaps or Annotations to a Heatmap List%v% pct_v_pct
Horizontally Add Heatmaps or Annotations to a Heatmap List+.AdditiveUnit add.AdditiveUnit
Method dispatch page for add_heatmapadd_heatmap
Add Heatmap to the Heatmap Listadd_heatmap,Heatmap-method
Add Annotations or Heatmaps as a Heatmap Listadd_heatmap,HeatmapAnnotation-method
Add heatmaps and row annotations to the heatmap listadd_heatmap,HeatmapList-method
Constructor Method for AdditiveUnit ClassAdditiveUnit
Class for Concatenating Heatmaps and AnnotationsAdditiveUnit-class
Adjust the Positions of nodes/leaves in the Dendrogramadjust_dend_by_x
Adjust Heatmap Listadjust_heatmap_list adjust_heatmap_list,HeatmapList-method
Automatically generate alter_funalter_graphic
Barplot Annotationanno_barplot
Block annotationanno_block
Boxplot Annotationanno_boxplot
Customized annotationanno_customize
Density Annotationanno_density
Empty Annotationanno_empty
Histogram Annotationanno_histogram
Horizon chart Annotationanno_horizon
Image Annotationanno_image
Joyplot Annotationanno_joyplot
Lines Annotationanno_lines
Link Annotationanno_link
Link annotation with labelsanno_mark
Numeric labels annotationanno_numeric
Barplot Annotation for oncoPrintanno_oncoprint_barplot
Points Annotationanno_points
Simple Annotationanno_simple
Summary Annotationanno_summary
Text Annotationanno_text
Text box annotationsanno_textbox
Zoom annotationanno_zoom
Grob for Annotation Axisannotation_axis_grob
Size of the Annotation Legendsannotation_legend_size annotation_legend_size,HeatmapList-method
Constructor of AnnotationFunction ClassAnnotationFunction
The AnnotationFunction ClassAnnotationFunction-class
Attach heatmap annotations to the heatmapattach_annotation attach_annotation,Heatmap-method
Draw 3D barsbar3D
Bin the genomebin_genome
Concatenate A List of ColorMapping objectsc.ColorMapping
Concatenate Heatmap Annotationsc.HeatmapAnnotation
Cluster only between Groupscluster_between_groups
Cluster within and between Groupscluster_within_group
Draw Legend Based on Color Mappingcolor_mapping_legend color_mapping_legend,ColorMapping-method
Constructor Method for ColorMapping ClassColorMapping
Class for Color MappingColorMapping-class
Method dispatch page for column_dendcolumn_dend
Get Column Dendrograms from a Heatmapcolumn_dend,Heatmap-method
Get Column Dendrograms from a hHeatmap Listcolumn_dend,HeatmapList-method
Method dispatch page for column_ordercolumn_order
Get Column Order from a Aeatmap Listcolumn_order,Heatmap-method
Get Column Order from a Heatmap Listcolumn_order,HeatmapList-method
Construct Column AnnotationscolumnAnnotation
Degrees of the Combination setscomb_degree
Names of the Combination setscomb_name
Sizes of the Combination setscomb_size
Compare heatmaps between stats::heatmap() and ComplexHeatmap::heatmap()compare_heatmap
Compare heatmaps between gplots::heatmap.2() and ComplexHeatmap::heatmap()compare_heatmap.2
Compare heatmaps between pheatmap::pheatmap() and ComplexHeatmap::pheatmap()compare_pheatmap
Complement Set Sizecomplement_size
Method dispatch page for component_heightcomponent_height
Heights of Heatmap Componentscomponent_height,Heatmap-method
Height of Heatmap List Componentscomponent_height,HeatmapList-method
Method dispatch page for component_widthcomponent_width
Widths of Heatmap Componentscomponent_width,Heatmap-method
Width of Heatmap List Componentscomponent_width,HeatmapList-method
Copy the AnnotationFunction Objectcopy_all,AnnotationFunction-method
Method dispatch page for copy_allcopy_all
Copy the SingleAnnotation objectcopy_all,SingleAnnotation-method
Decorate Heatmap Annotationdecorate_annotation
Decorate Heatmap Column Dendrogramsdecorate_column_dend
Decorate Heatmap Column Namesdecorate_column_names
Decorate Heatmap Column Titlesdecorate_column_title
Decorate Heatmap Dendrogramsdecorate_dend
Decorate Heatmap Dimension Namesdecorate_dimnames
Decorate Heatmap Bodiesdecorate_heatmap_body
Decorate Heatmap Row Dendrogramsdecorate_row_dend
Decorate Heatmap Row Namesdecorate_row_names
Decorate Heatmap Row Titlesdecorate_row_title
Decorate Heatmap Titlesdecorate_title
The Default Parameters for Annotation Axisdefault_axis_param
Default get_type for oncoPrint()default_get_type
Height of the Dendrogramsdend_heights
Coordinates of the Dendrogramdend_xy
Grob for DendrogramdendrogramGrob
Visualize Density Distribution by HeatmapdensityHeatmap
Dimension of the Heatmapdim.Heatmap
Calculate Pairwise Distance from a Matrixdist2
Draw legends for All Annotationsdraw_annotation_legend draw_annotation_legend,HeatmapList-method
Draw Heatmap Annotations on the Heatmapdraw_annotation draw_annotation,Heatmap-method
Draw Heatmap Dendrogramsdraw_dend draw_dend,Heatmap-method
Draw row names or column namesdraw_dimnames draw_dimnames,Heatmap-method
Draw Heatmap Bodydraw_heatmap_body draw_heatmap_body,Heatmap-method
Draw legends for All Heatmapsdraw_heatmap_legend draw_heatmap_legend,HeatmapList-method
Draw the List of Heatmapsdraw_heatmap_list draw_heatmap_list,HeatmapList-method
Method dispatch page for draw_titledraw_title
Draw Heatmap Titledraw_title,Heatmap-method
Draw Heatmap List Titledraw_title,HeatmapList-method
Draw the AnnotationFunction Objectdraw,AnnotationFunction-method
Method dispatch page for drawdraw
Draw a Single Heatmapdraw,Heatmap-method
Draw the Heatmap Annotationsdraw,HeatmapAnnotation-method
Draw a list of heatmapsdraw,HeatmapList-method
Draw the Legendsdraw,Legends-method
Draw the Single Annotationdraw,SingleAnnotation-method
Extract Elements in a Combination setextract_comb
Visualize Frequency Distribution by HeatmapfrequencyHeatmap
Full set of code of combination setsfull_comb_code
Get a List of ColorMapping objectsget_color_mapping_list get_color_mapping_list,HeatmapAnnotation-method
Get a List of Annotation Legend Parametersget_legend_param_list get_legend_param_list,HeatmapAnnotation-method
Convert XY in a Parent ViewportgetXY_in_parent_vp
Draw Annotation Axisgrid.annotation_axis
Draw a Single Boxplotgrid.boxplot
Draw the Dendrogramgrid.dendrogram
Draw the Legendsgrid.draw.Legends
Draw multiple texts in a boxgrid.textbox
Mark the text for the rendering by gridtext packagegt_render
Constructor method for Heatmap classHeatmap
Size of the Heatmap Legendsheatmap_legend_size heatmap_legend_size,HeatmapList-method
Class for a Single HeatmapHeatmap-class
3D HeatmapHeatmap3D
Constructor Method for HeatmapAnnotation classHeatmapAnnotation
Class for Heatmap AnnotationsHeatmapAnnotation-class
Constructor method for HeatmapList classHeatmapList
Class for a list of heatmapsHeatmapList-class
Height of the AnnotationFunction Objectheight.AnnotationFunction
Height of the Heatmapheight.Heatmap
Height of the HeatmapAnnotation Objectheight.HeatmapAnnotation
Height of the Heatmap Listheight.HeatmapList
Height of the Legendsheight.Legends
Height of the SingleAnnotation objectheight.SingleAnnotation
Assign the Height to the AnnotationFunction Objectheight<-.AnnotationFunction heightAssign.AnnotationFunction
Assign the Height to the HeatmapAnnotation Objectheight<-.HeatmapAnnotation heightAssign.HeatmapAnnotation
Assign the Height to the SingleAnnotation Objectheight<-.SingleAnnotation heightAssign.SingleAnnotation
Height for annotation_axis GrobheightDetails.annotation_axis
Grob height for packed_legendsheightDetails.legend
Grob height for legend_bodyheightDetails.legend_body
Grob height for packed_legendsheightDetails.packed_legends
Height for textbox grobheightDetails.textbox
Global Options for Heatmapsht_global_opt
Global Options for Heatmapsht_opt
Calculate the width and height of the heatmapsht_size
Test Whether it is an Absolute Unitis_abs_unit
Make a Single LegendLegend
Constructor method for Legends classLegends
The Class for LegendsLegends-class
Number of Annotationslength.HeatmapAnnotation
Length of the HeatmapList objectlength.HeatmapList
List All Heatmap Componentslist_components
Convert a List of Sets to a Binary Matrixlist_to_matrix
Make Cluster on Columnsmake_column_cluster make_column_cluster,Heatmap-method
Make a Combination Matrix for UpSet Plotmake_comb_mat
Method dispatch page for make_layoutmake_layout
Make the Layout of a Single Heatmapmake_layout,Heatmap-method
Make Layout for the Heatmap Listmake_layout,HeatmapList-method
Make Cluster on Rowsmake_row_cluster make_row_cluster,Heatmap-method
Map Values to Colorsmap_to_colors map_to_colors,ColorMapping-method
Maximum Height of Textmax_text_height
Maximum Width of Textmax_text_width
Merge Dendrogramsmerge_dendrogram
Annotation Namesnames.HeatmapAnnotation
Names of the heatmaps/annotationsnames.HeatmapList
Assign Annotation Namesnames<-.HeatmapAnnotation namesAssign.HeatmapAnnotation
Number of Columns in the Heatmapncol.Heatmap
Number of Observationsnobs.AnnotationFunction
Number of Observationsnobs.HeatmapAnnotation
Number of Observationsnobs.SingleAnnotation
Normalize a list of combination matricenormalize_comb_mat
Overlap genomic signals to the genomic binsnormalize_genomic_signals_to_bins
Number of Rows in the Heatmapnrow.Heatmap
Make oncoPrintoncoPrint
Order of the Combination Setsorder.comb_mat
Pack LegendspackLegend
Translate pheatmap::pheatmap to ComplexHeatmap::Heatmappheatmap
Get Values in a Matrix by Pair-wise Indicespindex
Draw heatmapplot.Heatmap
Draw heatmap annotationsplot.HeatmapAnnotation
Draw heatmapplot.HeatmapList
Prepare the Heatmapprepare prepare,Heatmap-method
Print the comb_mat Objectprint.comb_mat
Resize the Width or Height of Heatmap Annotationsre_size re_size,HeatmapAnnotation-method
Restore the index vector to index matrix in layer_funrestore_matrix
Barplots as Row Annotationrow_anno_barplot
Boxplots as Row Annotationrow_anno_boxplot
Density as Row Annotationrow_anno_density
Histograms as Row Annotationrow_anno_histogram
Points as Row Annotationrow_anno_points
Text as Row Annotationrow_anno_text
Method dispatch page for row_dendrow_dend
Get Row Dendrograms from a Heatmaprow_dend,Heatmap-method
Get Row Dendrograms from a Heatmap Listrow_dend,HeatmapList-method
Method dispatch page for row_orderrow_order
Get Row Order from a Heatmaprow_order,Heatmap-method
Get Row Order from a Heatmap Listrow_order,HeatmapList-method
Construct Row AnnotationsrowAnnotation
Set Height of Heatmap Componentset_component_height set_component_height,Heatmap-method
Set Width of Heatmap Componentset_component_width set_component_width,Heatmap-method
Set Namesset_name
Modify Set Namesset_name<- set_nameAssign
Set Sizesset_size
Print the AnnotationFunction Objectshow,AnnotationFunction-method
Print the ColorMapping Objectshow,ColorMapping-method
Method dispatch page for showshow
Draw the Single Heatmap with Defaultsshow,Heatmap-method
Print the HeatmapAnnotation objectshow,HeatmapAnnotation-method
Draw a list of heatmaps with default parametersshow,HeatmapList-method
Print the SingleAnnotation objectshow,SingleAnnotation-method
Constructor Method for SingleAnnotation ClassSingleAnnotation
Class for a Single AnnotationSingleAnnotation-class
Size of the AnnotationFunction Objectsize.AnnotationFunction
Size of the HeatmapAnnotation Objectsize.HeatmapAnnotation
Size of the SingleAnnotation Objectsize.SingleAnnotation
Assign the Size to the AnnotationFunction Objectsize<-.AnnotationFunction sizeAssign.AnnotationFunction
Assign the Size to the HeatmapAnnotation Objectsize<-.HeatmapAnnotation sizeAssign.HeatmapAnnotation
Assign the Size to the SingleAnnotation Objectsize<-.SingleAnnotation sizeAssign.SingleAnnotation
Adjust positions of rectanglar shapessmartAlign2
str methodstr.comb_mat
Subset a gpar Objectsubset_gp
Subset the Matrix by Rowssubset_matrix_by_row
Do not do subsetingsubset_no
Subset the vectorsubset_vector
Print the Summary of a Heatmapsummary.Heatmap
Summary of a Heatmap Listsummary.HeatmapList
Transpost the Combination Matrixt.comb_mat
Test alter_fun for oncoPrint()test_alter_fun
A simple grob for the word cloudtextbox_grob
Unify a List of Matrixunify_mat_list
Make the UpSet plotUpSet
UpSet Left Annotationupset_left_annotation
Default UpSet Right Annotationupset_right_annotation
Default UpSet Top Annotationupset_top_annotation
Width of the AnnotationFunction Objectwidth.AnnotationFunction
Width of the Heatmapwidth.Heatmap
Width of the HeatmapAnnotation Objectwidth.HeatmapAnnotation
Width of the Heatmap Listwidth.HeatmapList
Width of the Legendswidth.Legends
Width of the SingleAnnotation Objectwidth.SingleAnnotation
Assign the Width to the AnnotationFunction Objectwidth<-.AnnotationFunction widthAssign.AnnotationFunction
Assign the Width to the HeatmapAnnotation Objectwidth<-.HeatmapAnnotation widthAssign.HeatmapAnnotation
Assign the Width to the SingleAnnotation Objectwidth<-.SingleAnnotation widthAssign.SingleAnnotation
Width for annotation_axis GrobwidthDetails.annotation_axis
Grob width for packed_legendswidthDetails.legend
Grob width for legend_bodywidthDetails.legend_body
Grob width for packed_legendswidthDetails.packed_legends
Width for textbox grobwidthDetails.textbox