| Make complex heatmaps | ComplexHeatmap-package |
| Subset an AnnotationFunction Object | Extract.AnnotationFunction [.AnnotationFunction |
| Subset the Combination Matrix | Extract.comb_mat [.comb_mat |
| Subset method of gridtext class | Extract.gridtext [.gridtext |
| Subset a Heatmap | Extract.Heatmap [.Heatmap |
| Subset the HeatmapAnnotation object | Extract.HeatmapAnnotation [.HeatmapAnnotation |
| Subset a HeatmapList object | Extract.HeatmapList [.HeatmapList |
| Subset an SingleAnnotation Object | Extract.SingleAnnotation [.SingleAnnotation |
| Vertically Add Heatmaps or Annotations to a Heatmap List | %v% pct_v_pct |
| Horizontally Add Heatmaps or Annotations to a Heatmap List | +.AdditiveUnit add.AdditiveUnit |
| Method dispatch page for add_heatmap | add_heatmap |
| Add Heatmap to the Heatmap List | add_heatmap,Heatmap-method |
| Add Annotations or Heatmaps as a Heatmap List | add_heatmap,HeatmapAnnotation-method |
| Add heatmaps and row annotations to the heatmap list | add_heatmap,HeatmapList-method |
| Constructor Method for AdditiveUnit Class | AdditiveUnit |
| Class for Concatenating Heatmaps and Annotations | AdditiveUnit-class |
| Adjust the Positions of nodes/leaves in the Dendrogram | adjust_dend_by_x |
| Adjust Heatmap List | adjust_heatmap_list adjust_heatmap_list,HeatmapList-method |
| Automatically generate alter_fun | alter_graphic |
| Barplot Annotation | anno_barplot |
| Block annotation | anno_block |
| Boxplot Annotation | anno_boxplot |
| Customized annotation | anno_customize |
| Density Annotation | anno_density |
| Empty Annotation | anno_empty |
| Histogram Annotation | anno_histogram |
| Horizon chart Annotation | anno_horizon |
| Image Annotation | anno_image |
| Joyplot Annotation | anno_joyplot |
| Lines Annotation | anno_lines |
| Link Annotation | anno_link |
| Link annotation with labels | anno_mark |
| Numeric labels annotation | anno_numeric |
| Barplot Annotation for oncoPrint | anno_oncoprint_barplot |
| Points Annotation | anno_points |
| Simple Annotation | anno_simple |
| Summary Annotation | anno_summary |
| Text Annotation | anno_text |
| Text box annotations | anno_textbox |
| Zoom annotation | anno_zoom |
| Grob for Annotation Axis | annotation_axis_grob |
| Size of the Annotation Legends | annotation_legend_size annotation_legend_size,HeatmapList-method |
| Constructor of AnnotationFunction Class | AnnotationFunction |
| The AnnotationFunction Class | AnnotationFunction-class |
| Attach heatmap annotations to the heatmap | attach_annotation attach_annotation,Heatmap-method |
| Draw 3D bars | bar3D |
| Bin the genome | bin_genome |
| Concatenate A List of ColorMapping objects | c.ColorMapping |
| Concatenate Heatmap Annotations | c.HeatmapAnnotation |
| Cluster only between Groups | cluster_between_groups |
| Cluster within and between Groups | cluster_within_group |
| Draw Legend Based on Color Mapping | color_mapping_legend color_mapping_legend,ColorMapping-method |
| Constructor Method for ColorMapping Class | ColorMapping |
| Class for Color Mapping | ColorMapping-class |
| Method dispatch page for column_dend | column_dend |
| Get Column Dendrograms from a Heatmap | column_dend,Heatmap-method |
| Get Column Dendrograms from a hHeatmap List | column_dend,HeatmapList-method |
| Method dispatch page for column_order | column_order |
| Get Column Order from a Aeatmap List | column_order,Heatmap-method |
| Get Column Order from a Heatmap List | column_order,HeatmapList-method |
| Construct Column Annotations | columnAnnotation |
| Degrees of the Combination sets | comb_degree |
| Names of the Combination sets | comb_name |
| Sizes of the Combination sets | comb_size |
| Compare heatmaps between stats::heatmap() and ComplexHeatmap::heatmap() | compare_heatmap |
| Compare heatmaps between gplots::heatmap.2() and ComplexHeatmap::heatmap() | compare_heatmap.2 |
| Compare heatmaps between pheatmap::pheatmap() and ComplexHeatmap::pheatmap() | compare_pheatmap |
| Complement Set Size | complement_size |
| Method dispatch page for component_height | component_height |
| Heights of Heatmap Components | component_height,Heatmap-method |
| Height of Heatmap List Components | component_height,HeatmapList-method |
| Method dispatch page for component_width | component_width |
| Widths of Heatmap Components | component_width,Heatmap-method |
| Width of Heatmap List Components | component_width,HeatmapList-method |
| Copy the AnnotationFunction Object | copy_all,AnnotationFunction-method |
| Method dispatch page for copy_all | copy_all |
| Copy the SingleAnnotation object | copy_all,SingleAnnotation-method |
| Decorate Heatmap Annotation | decorate_annotation |
| Decorate Heatmap Column Dendrograms | decorate_column_dend |
| Decorate Heatmap Column Names | decorate_column_names |
| Decorate Heatmap Column Titles | decorate_column_title |
| Decorate Heatmap Dendrograms | decorate_dend |
| Decorate Heatmap Dimension Names | decorate_dimnames |
| Decorate Heatmap Bodies | decorate_heatmap_body |
| Decorate Heatmap Row Dendrograms | decorate_row_dend |
| Decorate Heatmap Row Names | decorate_row_names |
| Decorate Heatmap Row Titles | decorate_row_title |
| Decorate Heatmap Titles | decorate_title |
| The Default Parameters for Annotation Axis | default_axis_param |
| Default get_type for oncoPrint() | default_get_type |
| Height of the Dendrograms | dend_heights |
| Coordinates of the Dendrogram | dend_xy |
| Grob for Dendrogram | dendrogramGrob |
| Visualize Density Distribution by Heatmap | densityHeatmap |
| Dimension of the Heatmap | dim.Heatmap |
| Calculate Pairwise Distance from a Matrix | dist2 |
| Draw legends for All Annotations | draw_annotation_legend draw_annotation_legend,HeatmapList-method |
| Draw Heatmap Annotations on the Heatmap | draw_annotation draw_annotation,Heatmap-method |
| Draw Heatmap Dendrograms | draw_dend draw_dend,Heatmap-method |
| Draw row names or column names | draw_dimnames draw_dimnames,Heatmap-method |
| Draw Heatmap Body | draw_heatmap_body draw_heatmap_body,Heatmap-method |
| Draw legends for All Heatmaps | draw_heatmap_legend draw_heatmap_legend,HeatmapList-method |
| Draw the List of Heatmaps | draw_heatmap_list draw_heatmap_list,HeatmapList-method |
| Method dispatch page for draw_title | draw_title |
| Draw Heatmap Title | draw_title,Heatmap-method |
| Draw Heatmap List Title | draw_title,HeatmapList-method |
| Draw the AnnotationFunction Object | draw,AnnotationFunction-method |
| Method dispatch page for draw | draw |
| Draw a Single Heatmap | draw,Heatmap-method |
| Draw the Heatmap Annotations | draw,HeatmapAnnotation-method |
| Draw a list of heatmaps | draw,HeatmapList-method |
| Draw the Legends | draw,Legends-method |
| Draw the Single Annotation | draw,SingleAnnotation-method |
| Extract Elements in a Combination set | extract_comb |
| Visualize Frequency Distribution by Heatmap | frequencyHeatmap |
| Full set of code of combination sets | full_comb_code |
| Get a List of ColorMapping objects | get_color_mapping_list get_color_mapping_list,HeatmapAnnotation-method |
| Get a List of Annotation Legend Parameters | get_legend_param_list get_legend_param_list,HeatmapAnnotation-method |
| Convert XY in a Parent Viewport | getXY_in_parent_vp |
| Draw Annotation Axis | grid.annotation_axis |
| Draw a Single Boxplot | grid.boxplot |
| Draw the Dendrogram | grid.dendrogram |
| Draw the Legends | grid.draw.Legends |
| Draw multiple texts in a box | grid.textbox |
| Mark the text for the rendering by gridtext package | gt_render |
| Constructor method for Heatmap class | Heatmap |
| Size of the Heatmap Legends | heatmap_legend_size heatmap_legend_size,HeatmapList-method |
| Class for a Single Heatmap | Heatmap-class |
| 3D Heatmap | Heatmap3D |
| Constructor Method for HeatmapAnnotation class | HeatmapAnnotation |
| Class for Heatmap Annotations | HeatmapAnnotation-class |
| Constructor method for HeatmapList class | HeatmapList |
| Class for a list of heatmaps | HeatmapList-class |
| Height of the AnnotationFunction Object | height.AnnotationFunction |
| Height of the Heatmap | height.Heatmap |
| Height of the HeatmapAnnotation Object | height.HeatmapAnnotation |
| Height of the Heatmap List | height.HeatmapList |
| Height of the Legends | height.Legends |
| Height of the SingleAnnotation object | height.SingleAnnotation |
| Assign the Height to the AnnotationFunction Object | height<-.AnnotationFunction heightAssign.AnnotationFunction |
| Assign the Height to the HeatmapAnnotation Object | height<-.HeatmapAnnotation heightAssign.HeatmapAnnotation |
| Assign the Height to the SingleAnnotation Object | height<-.SingleAnnotation heightAssign.SingleAnnotation |
| Height for annotation_axis Grob | heightDetails.annotation_axis |
| Grob height for packed_legends | heightDetails.legend |
| Grob height for legend_body | heightDetails.legend_body |
| Grob height for packed_legends | heightDetails.packed_legends |
| Height for textbox grob | heightDetails.textbox |
| Global Options for Heatmaps | ht_global_opt |
| Global Options for Heatmaps | ht_opt |
| Calculate the width and height of the heatmaps | ht_size |
| Test Whether it is an Absolute Unit | is_abs_unit |
| Make a Single Legend | Legend |
| Constructor method for Legends class | Legends |
| The Class for Legends | Legends-class |
| Number of Annotations | length.HeatmapAnnotation |
| Length of the HeatmapList object | length.HeatmapList |
| List All Heatmap Components | list_components |
| Convert a List of Sets to a Binary Matrix | list_to_matrix |
| Make Cluster on Columns | make_column_cluster make_column_cluster,Heatmap-method |
| Make a Combination Matrix for UpSet Plot | make_comb_mat |
| Method dispatch page for make_layout | make_layout |
| Make the Layout of a Single Heatmap | make_layout,Heatmap-method |
| Make Layout for the Heatmap List | make_layout,HeatmapList-method |
| Make Cluster on Rows | make_row_cluster make_row_cluster,Heatmap-method |
| Map Values to Colors | map_to_colors map_to_colors,ColorMapping-method |
| Maximum Height of Text | max_text_height |
| Maximum Width of Text | max_text_width |
| Merge Dendrograms | merge_dendrogram |
| Annotation Names | names.HeatmapAnnotation |
| Names of the heatmaps/annotations | names.HeatmapList |
| Assign Annotation Names | names<-.HeatmapAnnotation namesAssign.HeatmapAnnotation |
| Number of Columns in the Heatmap | ncol.Heatmap |
| Number of Observations | nobs.AnnotationFunction |
| Number of Observations | nobs.HeatmapAnnotation |
| Number of Observations | nobs.SingleAnnotation |
| Normalize a list of combination matrice | normalize_comb_mat |
| Overlap genomic signals to the genomic bins | normalize_genomic_signals_to_bins |
| Number of Rows in the Heatmap | nrow.Heatmap |
| Make oncoPrint | oncoPrint |
| Order of the Combination Sets | order.comb_mat |
| Pack Legends | packLegend |
| Translate pheatmap::pheatmap to ComplexHeatmap::Heatmap | pheatmap |
| Get Values in a Matrix by Pair-wise Indices | pindex |
| Draw heatmap | plot.Heatmap |
| Draw heatmap annotations | plot.HeatmapAnnotation |
| Draw heatmap | plot.HeatmapList |
| Prepare the Heatmap | prepare prepare,Heatmap-method |
| Print the comb_mat Object | print.comb_mat |
| Resize the Width or Height of Heatmap Annotations | re_size re_size,HeatmapAnnotation-method |
| Restore the index vector to index matrix in layer_fun | restore_matrix |
| Barplots as Row Annotation | row_anno_barplot |
| Boxplots as Row Annotation | row_anno_boxplot |
| Density as Row Annotation | row_anno_density |
| Histograms as Row Annotation | row_anno_histogram |
| Points as Row Annotation | row_anno_points |
| Text as Row Annotation | row_anno_text |
| Method dispatch page for row_dend | row_dend |
| Get Row Dendrograms from a Heatmap | row_dend,Heatmap-method |
| Get Row Dendrograms from a Heatmap List | row_dend,HeatmapList-method |
| Method dispatch page for row_order | row_order |
| Get Row Order from a Heatmap | row_order,Heatmap-method |
| Get Row Order from a Heatmap List | row_order,HeatmapList-method |
| Construct Row Annotations | rowAnnotation |
| Set Height of Heatmap Component | set_component_height set_component_height,Heatmap-method |
| Set Width of Heatmap Component | set_component_width set_component_width,Heatmap-method |
| Set Names | set_name |
| Modify Set Names | set_name<- set_nameAssign |
| Set Sizes | set_size |
| Print the AnnotationFunction Object | show,AnnotationFunction-method |
| Print the ColorMapping Object | show,ColorMapping-method |
| Method dispatch page for show | show |
| Draw the Single Heatmap with Defaults | show,Heatmap-method |
| Print the HeatmapAnnotation object | show,HeatmapAnnotation-method |
| Draw a list of heatmaps with default parameters | show,HeatmapList-method |
| Print the SingleAnnotation object | show,SingleAnnotation-method |
| Constructor Method for SingleAnnotation Class | SingleAnnotation |
| Class for a Single Annotation | SingleAnnotation-class |
| Size of the AnnotationFunction Object | size.AnnotationFunction |
| Size of the HeatmapAnnotation Object | size.HeatmapAnnotation |
| Size of the SingleAnnotation Object | size.SingleAnnotation |
| Assign the Size to the AnnotationFunction Object | size<-.AnnotationFunction sizeAssign.AnnotationFunction |
| Assign the Size to the HeatmapAnnotation Object | size<-.HeatmapAnnotation sizeAssign.HeatmapAnnotation |
| Assign the Size to the SingleAnnotation Object | size<-.SingleAnnotation sizeAssign.SingleAnnotation |
| Adjust positions of rectanglar shapes | smartAlign2 |
| str method | str.comb_mat |
| Subset a gpar Object | subset_gp |
| Subset the Matrix by Rows | subset_matrix_by_row |
| Do not do subseting | subset_no |
| Subset the vector | subset_vector |
| Print the Summary of a Heatmap | summary.Heatmap |
| Summary of a Heatmap List | summary.HeatmapList |
| Transpost the Combination Matrix | t.comb_mat |
| Test alter_fun for oncoPrint() | test_alter_fun |
| A simple grob for the word cloud | textbox_grob |
| Unify a List of Matrix | unify_mat_list |
| Make the UpSet plot | UpSet |
| UpSet Left Annotation | upset_left_annotation |
| Default UpSet Right Annotation | upset_right_annotation |
| Default UpSet Top Annotation | upset_top_annotation |
| Width of the AnnotationFunction Object | width.AnnotationFunction |
| Width of the Heatmap | width.Heatmap |
| Width of the HeatmapAnnotation Object | width.HeatmapAnnotation |
| Width of the Heatmap List | width.HeatmapList |
| Width of the Legends | width.Legends |
| Width of the SingleAnnotation Object | width.SingleAnnotation |
| Assign the Width to the AnnotationFunction Object | width<-.AnnotationFunction widthAssign.AnnotationFunction |
| Assign the Width to the HeatmapAnnotation Object | width<-.HeatmapAnnotation widthAssign.HeatmapAnnotation |
| Assign the Width to the SingleAnnotation Object | width<-.SingleAnnotation widthAssign.SingleAnnotation |
| Width for annotation_axis Grob | widthDetails.annotation_axis |
| Grob width for packed_legends | widthDetails.legend |
| Grob width for legend_body | widthDetails.legend_body |
| Grob width for packed_legends | widthDetails.packed_legends |
| Width for textbox grob | widthDetails.textbox |
