Man pages for jokergoo/ComplexHeatmap
Make Complex Heatmaps
| add.AdditiveUnit | Horizontally Add Heatmaps or Annotations to a Heatmap List |
| add_heatmap-dispatch | Method dispatch page for add_heatmap |
| 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 |
| add_heatmap-Heatmap-method | Add Heatmap to the Heatmap List |
| AdditiveUnit | Constructor Method for AdditiveUnit Class |
| AdditiveUnit-class | Class for Concatenating Heatmaps and Annotations |
| 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 |
| annotation_axis_grob | Grob for Annotation Axis |
| AnnotationFunction | Constructor of AnnotationFunction Class |
| AnnotationFunction-class | The AnnotationFunction Class |
| annotation_legend_size-HeatmapList-method | Size of the Annotation Legends |
| anno_text | Text Annotation |
| anno_textbox | Text box annotations |
| anno_zoom | Zoom annotation |
| 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 |
| ColorMapping | Constructor Method for ColorMapping Class |
| ColorMapping-class | Class for Color Mapping |
| color_mapping_legend-ColorMapping-method | Draw Legend Based on Color Mapping |
| columnAnnotation | Construct Column Annotations |
| column_dend-dispatch | Method dispatch page for column_dend |
| column_dend-HeatmapList-method | Get Column Dendrograms from a hHeatmap List |
| column_dend-Heatmap-method | Get Column Dendrograms from a Heatmap |
| column_order-dispatch | Method dispatch page for column_order |
| column_order-HeatmapList-method | Get Column Order from a Heatmap List |
| column_order-Heatmap-method | Get Column Order from a Aeatmap 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... |
| compare_heatmap.2 | Compare heatmaps between gplots::heatmap.2() and... |
| compare_pheatmap | Compare heatmaps between pheatmap::pheatmap() and... |
| complement_size | Complement Set Size |
| ComplexHeatmap-package | Make complex heatmaps |
| component_height-dispatch | Method dispatch page for component_height |
| component_height-HeatmapList-method | Height of Heatmap List Components |
| component_height-Heatmap-method | Heights of Heatmap Components |
| component_width-dispatch | Method dispatch page for component_width |
| component_width-HeatmapList-method | Width of Heatmap List Components |
| component_width-Heatmap-method | Widths of Heatmap Components |
| copy_all-AnnotationFunction-method | Copy the AnnotationFunction Object |
| copy_all-dispatch | Method dispatch page for copy_all |
| 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 |
| dendrogramGrob | Grob for Dendrogram |
| 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-AnnotationFunction-method | Draw the AnnotationFunction Object |
| 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-dispatch | Method dispatch page for draw |
| draw-HeatmapAnnotation-method | Draw the Heatmap Annotations |
| 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-HeatmapList-method | Draw a list of heatmaps |
| draw-Heatmap-method | Draw a Single Heatmap |
| draw-Legends-method | Draw the Legends |
| draw-SingleAnnotation-method | Draw the Single Annotation |
| draw_title-dispatch | Method dispatch page for draw_title |
| draw_title-HeatmapList-method | Draw Heatmap List Title |
| draw_title-Heatmap-method | Draw Heatmap Title |
| Extract.AnnotationFunction | Subset an AnnotationFunction Object |
| extract_comb | Extract Elements in a Combination set |
| 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 |
| frequencyHeatmap | Visualize Frequency Distribution by Heatmap |
| full_comb_code | Full set of code of combination sets |
| 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 |
| getXY_in_parent_vp | Convert XY in a Parent Viewport |
| 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 | Constructor method for Heatmap class |
| Heatmap3D | 3D Heatmap |
| HeatmapAnnotation | Constructor Method for HeatmapAnnotation class |
| HeatmapAnnotation-class | Class for Heatmap Annotations |
| Heatmap-class | Class for a Single Heatmap |
| heatmap_legend_size-HeatmapList-method | Size of the Heatmap Legends |
| HeatmapList | Constructor method for HeatmapList class |
| HeatmapList-class | Class for a list of heatmaps |
| height.AnnotationFunction | Height of the AnnotationFunction 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 |
| 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 |
| 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 |
| 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 |
| make_column_cluster-Heatmap-method | Make Cluster on Columns |
| make_comb_mat | Make a Combination Matrix for UpSet Plot |
| make_layout-dispatch | Method dispatch page for make_layout |
| make_layout-HeatmapList-method | Make Layout for the Heatmap List |
| make_layout-Heatmap-method | Make the Layout of a Single Heatmap |
| 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 |
| namesAssign.HeatmapAnnotation | Assign Annotation Names |
| names.HeatmapAnnotation | Annotation Names |
| names.HeatmapList | Names of the heatmaps/annotations |
| 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 |
| 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-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 |
| 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 |
| rowAnnotation | Construct Row Annotations |
| row_anno_text | Text as Row Annotation |
| row_dend-dispatch | Method dispatch page for row_dend |
| row_dend-HeatmapList-method | Get Row Dendrograms from a Heatmap List |
| row_dend-Heatmap-method | Get Row Dendrograms from a Heatmap |
| row_order-dispatch | Method dispatch page for row_order |
| row_order-HeatmapList-method | Get Row Order from a Heatmap List |
| row_order-Heatmap-method | Get Row Order from a Heatmap |
| 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-AnnotationFunction-method | Print the AnnotationFunction Object |
| show-ColorMapping-method | Print the ColorMapping Object |
| show-dispatch | Method dispatch page for show |
| show-HeatmapAnnotation-method | Print the HeatmapAnnotation object |
| show-HeatmapList-method | Draw a list of heatmaps with default parameters |
| show-Heatmap-method | Draw the Single Heatmap with Defaults |
| show-SingleAnnotation-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 |
| 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 |
| size.HeatmapAnnotation | Size of the HeatmapAnnotation Object |
| size.SingleAnnotation | Size of 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 | Make the UpSet plot |
| 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 |
| 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 |
| 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 |
