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