# Making Complex Heatmaps

## Documentation for package ‘ComplexHeatmap’ version 1.12.0

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

## Help Pages

A C D E G H I L M O P R S U misc

ComplexHeatmap-package | Making complex heatmap

## -- A --

AdditiveUnit | Constructor method for AdditiveUnit class
AdditiveUnit-class | An internal class
add_heatmap | Method dispatch page for add_heatmap
add_heatmap-method | Add heatmaps or row annotations as a heatmap list
add_heatmap-method | Add row annotations or heatmaps as a heatmap list
add_heatmap-method | Add heatmaps and row annotations to the heatmap list
annotation_legend_size | Size of the annotation legend viewport
annotation_legend_size-method | Size of the annotation legend viewport
anno_barplot | Using barplot as annotation
anno_boxplot | Using boxplot as annotation
anno_density | Using kernel density as annotation
anno_histogram | Using histogram as annotation
anno_link | Link annotation with labels
anno_oncoprint_barplot | Column barplot annotaiton for oncoPrint
anno_points | Using points as annotation
anno_text | Using text as annotation

## -- C --

ColorMapping | Constructor methods for ColorMapping class
ColorMapping-class | Class to map values to colors
color_mapping_legend | Draw legend based on color mapping
color_mapping_legend-method | Draw legend based on color mapping
columnAnnotation | Construct column annotations
column_anno_barplot | Column annotation which is represented as barplots
column_anno_boxplot | Column annotation which is represented as boxplots
column_anno_density | Column annotation which is represented as density plot
column_anno_histogram | Column annotation which is represented as histogram
column_anno_link | Column annotation which is represented as links
column_anno_points | Column annotation which is represented as points
column_anno_text | Column annotation which is represented as text
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 heatmap list
column_order | Method dispatch page for column_order
column_order-method | Get column order from a heatmap list
column_order-method | Get column order from a heatmap list
component_height | Method dispatch page for component_height
component_height-method | Height of each heatmap component
component_height-method | Height of each heatmap list component
component_width | Method dispatch page for component_width
component_width-method | Width of each heatmap component
component_width-method | Width of each heatmap list component

## -- D --

decorate_annotation | Decorate the heatmap annotation
decorate_column_dend | Decorate heatmap dendrogram on columns
decorate_column_names | Decorate heatmap column names
decorate_column_title | Decorate heatmap column title
decorate_dend | Decorate the heatmap dendrogram
decorate_dimnames | Decorate the heatmap dimension names
decorate_heatmap_body | Decorate the heatmap body
decorate_row_dend | Decorate heatmap dendrogram on rows
decorate_row_names | Decorate heatmap row names
decorate_row_title | Decorate heatmap row title
decorate_title | Decorate the heatmap title
densityHeatmap | Use colors to represent density distribution
dist2 | Calculate pairwise distance from a matrix
draw | Method dispatch page for draw
draw-method | Draw a single heatmap
draw-method | Draw the heatmap annotations
draw-method | Draw a list of heatmaps
draw-method | Draw the single annotation
draw_annotation | Draw column annotations
draw_annotation-method | Draw column annotations
draw_annotation_legend | Draw legends for all column annotations
draw_annotation_legend-method | Draw legends for all column annotations
draw_dend | Draw dendrogram on row or column
draw_dend-method | Draw dendrogram on row or column
draw_dimnames | Draw row names or column names
draw_dimnames-method | Draw row names or column names
draw_heatmap_body | Draw the heatmap body
draw_heatmap_body-method | Draw the 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 --

enhanced_basicplot | Enhanced version of basic barplot and boxplot

## -- G --

get_color_mapping_list | Get a list of color mapping objects
get_color_mapping_list-method | Get a list of color mapping objects
get_color_mapping_param_list | Get a list of color mapping parameters
get_color_mapping_param_list-method | Get a list of color mapping parameters
grid.dendrogram | Draw dendrogram under grid system

## -- H --

Heatmap | Constructor method for Heatmap class
Heatmap-class | Class for a single 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 legend viewport
heatmap_legend_size-method | Size of the heatmap legend viewport
ht_global_opt | Global graphic options for heatmaps

## -- I --

is_abs_unit | Whether the unit object contains absolute unit

## -- L --

Legend | Making legend grobs

## -- M --

make_column_cluster | Make cluster on columns
make_column_cluster-method | Make cluster on columns
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 complete plot
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

## -- O --

oncoPrint | Make oncoPrint

## -- P --

plotDataFrame | Quickly visualize a data frame
prepare | Prepare the heatmap
prepare-method | Prepare the heatmap

## -- R --

rowAnnotation | Construct row annotations
row_anno_barplot | Row annotation which is represented as barplots
row_anno_boxplot | Row annotation which is represented as boxplots
row_anno_density | Row annotation which is represented as density plot
row_anno_histogram | Row annotation which is represented as histogram
row_anno_link | Column annotation which is represented as links
row_anno_points | Row annotation which is represented as points
row_anno_text | Row annotation which is represented as text
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 --

selectArea | Select an area in the heatmap
set_component_height | Set height of each heatmap component
set_component_height-method | Set height of each heatmap component
show | Method dispatch page for show
show-method | Print ColorMapping object
show-method | Draw the single heatmap with default parameters
show-method | Print the Heatmap Annotation 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

## -- U --

unify_mat_list | Unify a list of matrix

## -- misc --

+.AdditiveUnit | Add heatmaps or row annotations to a heatmap list