%v% Vertically Add Heatmaps or Annotations to a
Heatmap List
+.AdditiveUnit Horizontally Add Heatmaps or Annotations to a
Heatmap List
AdditiveUnit Constructor Method for AdditiveUnit Class
AdditiveUnit-class Class for Concatenating Heatmaps and
Annotations
AnnotationFunction Constructor of AnnotationFunction Class
AnnotationFunction-class
The AnnotationFunction Class
ColorMapping Constructor Method for ColorMapping Class
ColorMapping-class Class for Color Mapping
ComplexHeatmap-package
Make complex heatmaps
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
Legend Make a Single Legend
Legends Constructor method for Legends class
Legends-class The Class for Legends
SingleAnnotation Constructor Method for SingleAnnotation Class
SingleAnnotation-class
Class for a Single Annotation
UpSet Make the UpSet plot
[.AnnotationFunction Subset an AnnotationFunction Object
[.Heatmap Subset a Heatmap
[.HeatmapAnnotation Subset the HeatmapAnnotation object
[.HeatmapList Subset a HeatmapList object
[.SingleAnnotation Subset an SingleAnnotation Object
[.comb_mat Subset the Combination Matrix
[.gridtext Subset method of gridtext class
add_heatmap Method dispatch page for add_heatmap
add_heatmap,Heatmap-method
Add Heatmap to the Heatmap List
add_heatmap,HeatmapAnnotation-method
Add Annotations or Heatmaps as a Heatmap List
add_heatmap,HeatmapList-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,HeatmapList-method
Adjust Heatmap List
alter_graphic Automatically generate alter_fun
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
annotation_axis_grob Grob for Annotation Axis
annotation_legend_size,HeatmapList-method
Size of the Annotation Legends
attach_annotation,Heatmap-method
Attach heatmap annotations to the heatmap
bar3D Draw 3D bars
bin_genome Bin the genome
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
color_mapping_legend,ColorMapping-method
Draw Legend Based on Color Mapping
columnAnnotation Construct Column Annotations
column_dend Method dispatch page for column_dend
column_dend,Heatmap-method
Get Column Dendrograms from a Heatmap
column_dend,HeatmapList-method
Get Column Dendrograms from a hHeatmap List
column_order Method dispatch page for column_order
column_order,Heatmap-method
Get Column Order from a Aeatmap List
column_order,HeatmapList-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,Heatmap-method
Heights of Heatmap Components
component_height,HeatmapList-method
Height of Heatmap List Components
component_width Method dispatch page for component_width
component_width,Heatmap-method
Widths of Heatmap Components
component_width,HeatmapList-method
Width of Heatmap List Components
copy_all Method dispatch page for copy_all
copy_all,AnnotationFunction-method
Copy the AnnotationFunction Object
copy_all,SingleAnnotation-method
Copy the SingleAnnotation object
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()
dend_heights Height of the Dendrograms
dend_xy Coordinates of the Dendrogram
dendrogramGrob Grob for 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,AnnotationFunction-method
Draw the AnnotationFunction Object
draw,Heatmap-method Draw a Single Heatmap
draw,HeatmapAnnotation-method
Draw the Heatmap Annotations
draw,HeatmapList-method
Draw a list of heatmaps
draw,Legends-method Draw the Legends
draw,SingleAnnotation-method
Draw the Single Annotation
draw_annotation,Heatmap-method
Draw Heatmap Annotations on the Heatmap
draw_annotation_legend,HeatmapList-method
Draw legends for All Annotations
draw_dend,Heatmap-method
Draw Heatmap Dendrograms
draw_dimnames,Heatmap-method
Draw row names or column names
draw_heatmap_body,Heatmap-method
Draw Heatmap Body
draw_heatmap_legend,HeatmapList-method
Draw legends for All Heatmaps
draw_heatmap_list,HeatmapList-method
Draw the List of Heatmaps
draw_title Method dispatch page for draw_title
draw_title,Heatmap-method
Draw Heatmap Title
draw_title,HeatmapList-method
Draw Heatmap List Title
extract_comb Extract Elements in a Combination set
frequencyHeatmap Visualize Frequency Distribution by Heatmap
full_comb_code Full set of code of combination sets
getXY_in_parent_vp Convert XY in a Parent Viewport
get_color_mapping_list,HeatmapAnnotation-method
Get a List of ColorMapping objects
get_legend_param_list,HeatmapAnnotation-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
heatmap_legend_size,HeatmapList-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
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
is_abs_unit Test Whether it is an Absolute Unit
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
make_column_cluster,Heatmap-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,Heatmap-method
Make the Layout of a Single Heatmap
make_layout,HeatmapList-method
Make Layout for the Heatmap List
make_row_cluster,Heatmap-method
Make Cluster on Rows
map_to_colors,ColorMapping-method
Map Values to Colors
max_text_height Maximum Height of Text
max_text_width Maximum Width of Text
merge_dendrogram Merge Dendrograms
names.HeatmapAnnotation
Annotation Names
names.HeatmapList Names of the heatmaps/annotations
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
oncoPrint Make oncoPrint
order.comb_mat Order of the Combination Sets
packLegend Pack Legends
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,Heatmap-method
Prepare the Heatmap
print.comb_mat Print the comb_mat Object
re_size,HeatmapAnnotation-method
Resize the Width or Height of Heatmap
Annotations
restore_matrix Restore the index vector to index matrix in
layer_fun
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,Heatmap-method
Get Row Dendrograms from a Heatmap
row_dend,HeatmapList-method
Get Row Dendrograms from a Heatmap List
row_order Method dispatch page for row_order
row_order,Heatmap-method
Get Row Order from a Heatmap
row_order,HeatmapList-method
Get Row Order from a Heatmap List
set_component_height,Heatmap-method
Set Height of Heatmap Component
set_component_width,Heatmap-method
Set Width of Heatmap Component
set_name Set Names
set_nameAssign Modify Set Names
set_size Set Sizes
show Method dispatch page for show
show,AnnotationFunction-method
Print the AnnotationFunction Object
show,ColorMapping-method
Print the ColorMapping Object
show,Heatmap-method Draw the Single Heatmap with Defaults
show,HeatmapAnnotation-method
Print the HeatmapAnnotation object
show,HeatmapList-method
Draw a list of heatmaps with default parameters
show,SingleAnnotation-method
Print the SingleAnnotation object
size.AnnotationFunction
Size of the AnnotationFunction Object
size.HeatmapAnnotation
Size of the HeatmapAnnotation Object
size.SingleAnnotation Size of 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.comb_mat Transpost the Combination Matrix
test_alter_fun Test alter_fun for oncoPrint()
textbox_grob A simple grob for the word cloud
unify_mat_list Unify a List of Matrix
upset_left_annotation UpSet Left Annotation
upset_right_annotation
Default UpSet Right Annotation
upset_top_annotation Default UpSet Top Annotation
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
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