%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
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
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
anno_barplot            Barplot Annotation
anno_block              Block annotation
anno_boxplot            Boxplot 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               Label Markers 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
annotation_axis_grob    Grob for Annotation Axis
annotation_legend_size,HeatmapList-method
                        Size of the Annotation Legends
c.HeatmapAnnotation     Concatenate Heatmap Annotations
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
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
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
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
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
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
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
names<-.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
nrow.Heatmap            Number of Rows in the Heatmap
oncoPrint               Make oncoPrint
order.comb_mat          Order of the Combination Sets
packLegend              Pack Legends
pindex                  Get Values in a Matrix by Pair-wise Indices
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_link           Label Markers 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_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
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
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_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()
unify_mat_list          Unify a List of Matrix
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
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
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
