Making Complex Heatmaps


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Documentation for package ‘ComplexHeatmap’ version 1.10.2

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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_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