Make Complex Heatmaps

Documentation for package ‘ComplexHeatmap’ version 2.10.0

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

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_oncoprint_barplot	Barplot Annotation for oncoPrint
anno_points	Points Annotation
anno_simple	Simple Annotation
anno_summary	Summary Annotation
anno_text	Text Annotation
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
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
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()

-- 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

-- 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