# Make Complex Heatmaps

## Documentation for package ‘ComplexHeatmap’ version 2.17.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A B C D E F G H I L M N O P R S T U W misc

ComplexHeatmap-package | Make complex heatmaps

## -- A --

add.AdditiveUnit | Horizontally Add Heatmaps or Annotations to a Heatmap List
AdditiveUnit | Constructor Method for AdditiveUnit Class
AdditiveUnit-class | Class for Concatenating Heatmaps and Annotations
add_heatmap | Method dispatch page for add_heatmap
add_heatmap-method | Add Heatmap to the Heatmap List
add_heatmap-method | Add Annotations or Heatmaps as a Heatmap List
add_heatmap-method | Add heatmaps and row annotations to the heatmap list
adjust_dend_by_x | Adjust the Positions of nodes/leaves in the Dendrogram
adjust_heatmap_list | Adjust Heatmap List
adjust_heatmap_list-method | Adjust Heatmap List
alter_graphic | Automatically generate alter_fun
AnnotationFunction | Constructor of AnnotationFunction Class
AnnotationFunction-class | The AnnotationFunction Class
annotation_axis_grob | Grob for Annotation Axis
annotation_legend_size | Size of the Annotation Legends
annotation_legend_size-method | Size of the Annotation Legends
anno_barplot | Barplot Annotation
anno_block | Block annotation
anno_boxplot | Boxplot Annotation
anno_customize | Customized annotation
anno_density | Density Annotation
anno_empty | Empty Annotation
anno_histogram | Histogram Annotation
anno_horizon | Horizon chart Annotation
anno_image | Image Annotation
anno_joyplot | Joyplot Annotation
anno_lines | Lines Annotation
anno_link | Link Annotation
anno_mark | Link annotation with labels
anno_numeric | Numeric labels annotation
anno_oncoprint_barplot | Barplot Annotation for oncoPrint
anno_points | Points Annotation
anno_simple | Simple Annotation
anno_summary | Summary Annotation
anno_text | Text Annotation
anno_textbox | Text box annotations
anno_zoom | Zoom annotation
attach_annotation | Attach heatmap annotations to the heatmap
attach_annotation-method | Attach heatmap annotations to the heatmap

## -- B --

bar3D | Draw 3D bars
bin_genome | Bin the genome

## -- C --

c.ColorMapping | Concatenate A List of ColorMapping objects
c.HeatmapAnnotation | Concatenate Heatmap Annotations
cluster_between_groups | Cluster only between Groups
cluster_within_group | Cluster within and between Groups
ColorMapping | Constructor Method for ColorMapping Class
ColorMapping-class | Class for Color Mapping
color_mapping_legend | Draw Legend Based on Color Mapping
color_mapping_legend-method | Draw Legend Based on Color Mapping
columnAnnotation | Construct Column Annotations
column_dend | Method dispatch page for column_dend
column_dend-method | Get Column Dendrograms from a Heatmap
column_dend-method | Get Column Dendrograms from a hHeatmap List
column_order | Method dispatch page for column_order
column_order-method | Get Column Order from a Aeatmap List
column_order-method | Get Column Order from a Heatmap List
comb_degree | Degrees of the Combination sets
comb_name | Names of the Combination sets
comb_size | Sizes of the Combination sets
compare_heatmap | Compare heatmaps between stats::heatmap() and ComplexHeatmap::heatmap()
compare_heatmap.2 | Compare heatmaps between gplots::heatmap.2() and ComplexHeatmap::heatmap()
compare_pheatmap | Compare heatmaps between pheatmap::pheatmap() and ComplexHeatmap::pheatmap()
complement_size | Complement Set Size
component_height | Method dispatch page for component_height
component_height-method | Heights of Heatmap Components
component_height-method | Height of Heatmap List Components
component_width | Method dispatch page for component_width
component_width-method | Widths of Heatmap Components
component_width-method | Width of Heatmap List Components
copy_all | Method dispatch page for copy_all
copy_all-method | Copy the AnnotationFunction Object
copy_all-method | Copy the SingleAnnotation object

## -- D --

decorate_annotation | Decorate Heatmap Annotation
decorate_column_dend | Decorate Heatmap Column Dendrograms
decorate_column_names | Decorate Heatmap Column Names
decorate_column_title | Decorate Heatmap Column Titles
decorate_dend | Decorate Heatmap Dendrograms
decorate_dimnames | Decorate Heatmap Dimension Names
decorate_heatmap_body | Decorate Heatmap Bodies
decorate_row_dend | Decorate Heatmap Row Dendrograms
decorate_row_names | Decorate Heatmap Row Names
decorate_row_title | Decorate Heatmap Row Titles
decorate_title | Decorate Heatmap Titles
default_axis_param | The Default Parameters for Annotation Axis
default_get_type | Default get_type for oncoPrint()
dendrogramGrob | Grob for Dendrogram
dend_heights | Height of the Dendrograms
dend_xy | Coordinates of the Dendrogram
densityHeatmap | Visualize Density Distribution by Heatmap
dim.Heatmap | Dimension of the Heatmap
dist2 | Calculate Pairwise Distance from a Matrix
draw | Method dispatch page for draw
draw-method | Draw the AnnotationFunction Object
draw-method | Draw a Single Heatmap
draw-method | Draw the Heatmap Annotations
draw-method | Draw a list of heatmaps
draw-method | Draw the Legends
draw-method | Draw the Single Annotation
draw_annotation | Draw Heatmap Annotations on the Heatmap
draw_annotation-method | Draw Heatmap Annotations on the Heatmap
draw_annotation_legend | Draw legends for All Annotations
draw_annotation_legend-method | Draw legends for All Annotations
draw_dend | Draw Heatmap Dendrograms
draw_dend-method | Draw Heatmap Dendrograms
draw_dimnames | Draw row names or column names
draw_dimnames-method | Draw row names or column names
draw_heatmap_body | Draw Heatmap Body
draw_heatmap_body-method | Draw Heatmap Body
draw_heatmap_legend | Draw legends for All Heatmaps
draw_heatmap_legend-method | Draw legends for All Heatmaps
draw_heatmap_list | Draw the List of Heatmaps
draw_heatmap_list-method | Draw the List of Heatmaps
draw_title | Method dispatch page for draw_title
draw_title-method | Draw Heatmap Title
draw_title-method | Draw Heatmap List Title

## -- E --

Extract.AnnotationFunction | Subset an AnnotationFunction Object
Extract.comb_mat | Subset the Combination Matrix
Extract.gridtext | Subset method of gridtext class
Extract.Heatmap | Subset a Heatmap
Extract.HeatmapAnnotation | Subset the HeatmapAnnotation object
Extract.HeatmapList | Subset a HeatmapList object
Extract.SingleAnnotation | Subset an SingleAnnotation Object
extract_comb | Extract Elements in a Combination set

## -- F --

frequencyHeatmap | Visualize Frequency Distribution by Heatmap
full_comb_code | Full set of code of combination sets

## -- G --

getXY_in_parent_vp | Convert XY in a Parent Viewport
get_color_mapping_list | Get a List of ColorMapping objects
get_color_mapping_list-method | Get a List of ColorMapping objects
get_legend_param_list | Get a List of Annotation Legend Parameters
get_legend_param_list-method | Get a List of Annotation Legend Parameters
grid.annotation_axis | Draw Annotation Axis
grid.boxplot | Draw a Single Boxplot
grid.dendrogram | Draw the Dendrogram
grid.draw.Legends | Draw the Legends
grid.textbox | Draw multiple texts in a box
gt_render | Mark the text for the rendering by gridtext package

## -- H --

Heatmap | Constructor method for Heatmap class
Heatmap-class | Class for a Single Heatmap
Heatmap3D | 3D Heatmap
HeatmapAnnotation | Constructor Method for HeatmapAnnotation class
HeatmapAnnotation-class | Class for Heatmap Annotations
HeatmapList | Constructor method for HeatmapList class
HeatmapList-class | Class for a list of heatmaps
heatmap_legend_size | Size of the Heatmap Legends
heatmap_legend_size-method | Size of the Heatmap Legends
height.AnnotationFunction | Height of the AnnotationFunction Object
height.Heatmap | Height of the Heatmap
height.HeatmapAnnotation | Height of the HeatmapAnnotation Object
height.HeatmapList | Height of the Heatmap List
height.Legends | Height of the Legends
height.SingleAnnotation | Height of the SingleAnnotation object
height<-.AnnotationFunction | Assign the Height to the AnnotationFunction Object
height<-.HeatmapAnnotation | Assign the Height to the HeatmapAnnotation Object
height<-.SingleAnnotation | Assign the Height to the SingleAnnotation Object
heightAssign.AnnotationFunction | Assign the Height to the AnnotationFunction Object
heightAssign.HeatmapAnnotation | Assign the Height to the HeatmapAnnotation Object
heightAssign.SingleAnnotation | Assign the Height to the SingleAnnotation Object
heightDetails.annotation_axis | Height for annotation_axis Grob
heightDetails.legend | Grob height for packed_legends
heightDetails.legend_body | Grob height for legend_body
heightDetails.packed_legends | Grob height for packed_legends
heightDetails.textbox | Height for textbox grob
ht_global_opt | Global Options for Heatmaps
ht_opt | Global Options for Heatmaps
ht_size | Calculate the width and height of the heatmaps

## -- I --

is_abs_unit | Test Whether it is an Absolute Unit

## -- L --

Legend | Make a Single Legend
Legends | Constructor method for Legends class
Legends-class | The Class for Legends
length.HeatmapAnnotation | Number of Annotations
length.HeatmapList | Length of the HeatmapList object
list_components | List All Heatmap Components
list_to_matrix | Convert a List of Sets to a Binary Matrix

## -- M --

make_column_cluster | Make Cluster on Columns
make_column_cluster-method | Make Cluster on Columns
make_comb_mat | Make a Combination Matrix for UpSet Plot
make_layout | Method dispatch page for make_layout
make_layout-method | Make the Layout of a Single Heatmap
make_layout-method | Make Layout for the Heatmap List
make_row_cluster | Make Cluster on Rows
make_row_cluster-method | Make Cluster on Rows
map_to_colors | Map Values to Colors
map_to_colors-method | Map Values to Colors
max_text_height | Maximum Height of Text
max_text_width | Maximum Width of Text
merge_dendrogram | Merge Dendrograms

## -- N --

names.HeatmapAnnotation | Annotation Names
names.HeatmapList | Names of the heatmaps/annotations
names<-.HeatmapAnnotation | Assign Annotation Names
namesAssign.HeatmapAnnotation | Assign Annotation Names
ncol.Heatmap | Number of Columns in the Heatmap
nobs.AnnotationFunction | Number of Observations
nobs.HeatmapAnnotation | Number of Observations
nobs.SingleAnnotation | Number of Observations
normalize_comb_mat | Normalize a list of combination matrice
normalize_genomic_signals_to_bins | Overlap genomic signals to the genomic bins
nrow.Heatmap | Number of Rows in the Heatmap

## -- O --

oncoPrint | Make oncoPrint
order.comb_mat | Order of the Combination Sets

## -- P --

packLegend | Pack Legends
pct_v_pct | Vertically Add Heatmaps or Annotations to a Heatmap List
pheatmap | Translate pheatmap::pheatmap to ComplexHeatmap::Heatmap
pindex | Get Values in a Matrix by Pair-wise Indices
plot.Heatmap | Draw heatmap
plot.HeatmapAnnotation | Draw heatmap annotations
plot.HeatmapList | Draw heatmap
prepare | Prepare the Heatmap
prepare-method | Prepare the Heatmap
print.comb_mat | Print the comb_mat Object

## -- R --

restore_matrix | Restore the index vector to index matrix in layer_fun
re_size | Resize the Width or Height of Heatmap Annotations
re_size-method | Resize the Width or Height of Heatmap Annotations
rowAnnotation | Construct Row Annotations
row_anno_barplot | Barplots as Row Annotation
row_anno_boxplot | Boxplots as Row Annotation
row_anno_density | Density as Row Annotation
row_anno_histogram | Histograms as Row Annotation
row_anno_points | Points as Row Annotation
row_anno_text | Text as Row Annotation
row_dend | Method dispatch page for row_dend
row_dend-method | Get Row Dendrograms from a Heatmap
row_dend-method | Get Row Dendrograms from a Heatmap List
row_order | Method dispatch page for row_order
row_order-method | Get Row Order from a Heatmap
row_order-method | Get Row Order from a Heatmap List

## -- S --

set_component_height | Set Height of Heatmap Component
set_component_height-method | Set Height of Heatmap Component
set_component_width | Set Width of Heatmap Component
set_component_width-method | Set Width of Heatmap Component
set_name | Set Names
set_name<- | Modify Set Names
set_nameAssign | Modify Set Names
set_size | Set Sizes
show | Method dispatch page for show
show-method | Print the AnnotationFunction Object
show-method | Print the ColorMapping Object
show-method | Draw the Single Heatmap with Defaults
show-method | Print the HeatmapAnnotation object
show-method | Draw a list of heatmaps with default parameters
show-method | Print the SingleAnnotation object
SingleAnnotation | Constructor Method for SingleAnnotation Class
SingleAnnotation-class | Class for a Single Annotation
size.AnnotationFunction | Size of the AnnotationFunction Object
size.HeatmapAnnotation | Size of the HeatmapAnnotation Object
size.SingleAnnotation | Size of the SingleAnnotation Object
size<-.AnnotationFunction | Assign the Size to the AnnotationFunction Object
size<-.HeatmapAnnotation | Assign the Size to the HeatmapAnnotation Object
size<-.SingleAnnotation | Assign the Size to the SingleAnnotation Object
sizeAssign.AnnotationFunction | Assign the Size to the AnnotationFunction Object
sizeAssign.HeatmapAnnotation | Assign the Size to the HeatmapAnnotation Object
sizeAssign.SingleAnnotation | Assign the Size to the SingleAnnotation Object
smartAlign2 | Adjust positions of rectanglar shapes
str.comb_mat | str method
subset_gp | Subset a gpar Object
subset_matrix_by_row | Subset the Matrix by Rows
subset_no | Do not do subseting
subset_vector | Subset the vector
summary.Heatmap | Print the Summary of a Heatmap
summary.HeatmapList | Summary of a Heatmap List

## -- T --

t.comb_mat | Transpost the Combination Matrix
test_alter_fun | Test alter_fun for oncoPrint()
textbox_grob | A simple grob for the word cloud

## -- U --

unify_mat_list | Unify a List of Matrix
UpSet | Make the UpSet plot
upset_left_annotation | UpSet Left Annotation
upset_right_annotation | Default UpSet Right Annotation
upset_top_annotation | Default UpSet Top Annotation

## -- W --

width.AnnotationFunction | Width of the AnnotationFunction Object
width.Heatmap | Width of the Heatmap
width.HeatmapAnnotation | Width of the HeatmapAnnotation Object
width.HeatmapList | Width of the Heatmap List
width.Legends | Width of the Legends
width.SingleAnnotation | Width of the SingleAnnotation Object
width<-.AnnotationFunction | Assign the Width to the AnnotationFunction Object
width<-.HeatmapAnnotation | Assign the Width to the HeatmapAnnotation Object
width<-.SingleAnnotation | Assign the Width to the SingleAnnotation Object
widthAssign.AnnotationFunction | Assign the Width to the AnnotationFunction Object
widthAssign.HeatmapAnnotation | Assign the Width to the HeatmapAnnotation Object
widthAssign.SingleAnnotation | Assign the Width to the SingleAnnotation Object
widthDetails.annotation_axis | Width for annotation_axis Grob
widthDetails.legend | Grob width for packed_legends
widthDetails.legend_body | Grob width for legend_body
widthDetails.packed_legends | Grob width for packed_legends
widthDetails.textbox | Width for textbox grob

## -- misc --

%v% | Vertically Add Heatmaps or Annotations to a Heatmap List
+.AdditiveUnit | Horizontally Add Heatmaps or Annotations to a Heatmap List
[.AnnotationFunction | Subset an AnnotationFunction Object
[.comb_mat | Subset the Combination Matrix
[.gridtext | Subset method of gridtext class
[.Heatmap | Subset a Heatmap
[.HeatmapAnnotation | Subset the HeatmapAnnotation object
[.HeatmapList | Subset a HeatmapList object
[.SingleAnnotation | Subset an SingleAnnotation Object