All functions
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AdditiveUnit-class
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Class for Concatenating Heatmaps and Annotations |
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AdditiveUnit()
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Constructor Method for AdditiveUnit Class |
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AnnotationFunction-class
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The AnnotationFunction Class |
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AnnotationFunction()
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Constructor of AnnotationFunction Class |
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ColorMapping-class
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Class for Color Mapping |
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ColorMapping()
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Constructor Method for ColorMapping Class |
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ComplexHeatmap-package
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Make complex heatmaps |
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`[`(<AnnotationFunction>)
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Subset an AnnotationFunction Object |
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`[`(<Heatmap>)
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Subset a Heatmap |
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`[`(<HeatmapAnnotation>)
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Subset the HeatmapAnnotation object |
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`[`(<HeatmapList>)
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Subset a HeatmapList object |
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`[`(<SingleAnnotation>)
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Subset an SingleAnnotation Object |
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`[`(<comb_mat>)
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Subset the Combination Matrix |
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Heatmap-class
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Class for a Single Heatmap |
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Heatmap()
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Constructor method for Heatmap class |
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HeatmapAnnotation-class
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Class for Heatmap Annotations |
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HeatmapAnnotation()
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Constructor Method for HeatmapAnnotation class |
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HeatmapList-class
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Class for a list of heatmaps |
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HeatmapList()
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Constructor method for HeatmapList class |
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Legend()
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Make a Single Legend |
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Legends-class
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The Class for Legends |
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Legends()
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Constructor method for Legends class |
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SingleAnnotation-class
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Class for a Single Annotation |
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SingleAnnotation()
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Constructor Method for SingleAnnotation Class |
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UpSet()
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Make the UpSet plot |
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`+`(<AdditiveUnit>)
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Horizontally Add Heatmaps or Annotations to a Heatmap List |
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add_heatmap(<Heatmap>)
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Add Heatmap to the Heatmap List |
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add_heatmap(<HeatmapAnnotation>)
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Add Annotations or Heatmaps as a Heatmap List |
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add_heatmap(<HeatmapList>)
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Add heatmaps and row annotations to the heatmap list |
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add_heatmap-dispatch
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Method dispatch page for add_heatmap |
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adjust_dend_by_x()
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Adjust the Positions of nodes/leaves in the Dendrogram |
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adjust_heatmap_list(<HeatmapList>)
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Adjust Heatmap List |
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anno_barplot()
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Barplot Annotation |
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anno_block()
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Block annotation |
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anno_boxplot()
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Boxplot Annotation |
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anno_density()
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Density Annotation |
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anno_empty()
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Empty Annotation |
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anno_histogram()
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Histogram Annotation |
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anno_horizon()
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Horizon chart Annotation |
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anno_image()
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Image Annotation |
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anno_joyplot()
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Joyplot Annotation |
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anno_lines()
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Lines Annotation |
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anno_link()
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Label Markers Annotation |
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anno_mark()
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Link annotation with labels |
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anno_oncoprint_barplot()
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Barplot Annotation for oncoPrint |
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anno_points()
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Points Annotation |
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anno_simple()
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Simple Annotation |
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anno_summary()
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Summary Annotation |
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anno_text()
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Text Annotation |
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anno_zoom()
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Zoom annotation |
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annotation_axis_grob()
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Grob for Annotation Axis |
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annotation_legend_size(<HeatmapList>)
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Size of the Annotation Legends |
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c(<ColorMapping>)
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Concatenate A List of ColorMapping objects |
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c(<HeatmapAnnotation>)
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Concatenate Heatmap Annotations |
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cluster_within_group()
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Cluster within and between Groups |
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color_mapping_legend(<ColorMapping>)
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Draw Legend Based on Color Mapping |
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columnAnnotation()
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Construct Column Annotations |
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column_dend(<Heatmap>)
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Get Column Dendrograms from a Heatmap |
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column_dend(<HeatmapList>)
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Get Column Dendrograms from a hHeatmap List |
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column_dend-dispatch
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Method dispatch page for column_dend |
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column_order(<Heatmap>)
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Get Column Order from a Aeatmap List |
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column_order(<HeatmapList>)
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Get Column Order from a Heatmap List |
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column_order-dispatch
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Method dispatch page for column_order |
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comb_degree()
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Degrees of the Combination sets |
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comb_name()
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Names of the Combination sets |
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comb_size()
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Sizes of the Combination sets |
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component_height(<Heatmap>)
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Heights of Heatmap Components |
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component_height(<HeatmapList>)
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Height of Heatmap List Components |
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component_height-dispatch
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Method dispatch page for component_height |
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component_width(<Heatmap>)
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Widths of Heatmap Components |
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component_width(<HeatmapList>)
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Width of Heatmap List Components |
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component_width-dispatch
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Method dispatch page for component_width |
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copy_all(<AnnotationFunction>)
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Copy the AnnotationFunction Object |
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copy_all(<SingleAnnotation>)
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Copy the SingleAnnotation object |
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copy_all-dispatch
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Method dispatch page for copy_all |
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decorate_annotation()
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Decorate Heatmap Annotation |
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decorate_column_dend()
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Decorate Heatmap Column Dendrograms |
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decorate_column_names()
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Decorate Heatmap Column Names |
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decorate_column_title()
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Decorate Heatmap Column Titles |
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decorate_dend()
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Decorate Heatmap Dendrograms |
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decorate_dimnames()
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Decorate Heatmap Dimension Names |
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decorate_heatmap_body()
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Decorate Heatmap Bodies |
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decorate_row_dend()
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Decorate Heatmap Row Dendrograms |
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decorate_row_names()
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Decorate Heatmap Row Names |
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decorate_row_title()
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Decorate Heatmap Row Titles |
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decorate_title()
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Decorate Heatmap Titles |
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default_axis_param()
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The Default Parameters for Annotation Axis |
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default_get_type()
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Default get_type for oncoPrint() |
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dend_heights()
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Height of the Dendrograms |
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dend_xy()
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Coordinates of the Dendrogram |
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dendrogramGrob()
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Grob for Dendrogram |
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densityHeatmap()
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Visualize Density Distribution by Heatmap |
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dim(<Heatmap>)
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Dimension of the Heatmap |
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dist2()
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Calculate Pairwise Distance from a Matrix |
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draw(<AnnotationFunction>)
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Draw the AnnotationFunction Object |
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draw(<Heatmap>)
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Draw a Single Heatmap |
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draw(<HeatmapAnnotation>)
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Draw the Heatmap Annotations |
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draw(<HeatmapList>)
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Draw a list of heatmaps |
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draw(<Legends>)
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Draw the Legends |
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draw(<SingleAnnotation>)
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Draw the Single Annotation |
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draw-dispatch
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Method dispatch page for draw |
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draw_annotation(<Heatmap>)
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Draw Heatmap Annotations on the Heatmap |
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draw_annotation_legend(<HeatmapList>)
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Draw legends for All Annotations |
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draw_dend(<Heatmap>)
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Draw Heatmap Dendrograms |
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draw_dimnames(<Heatmap>)
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Draw row names or column names |
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draw_heatmap_body(<Heatmap>)
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Draw Heatmap Body |
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draw_heatmap_legend(<HeatmapList>)
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Draw legends for All Heatmaps |
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draw_heatmap_list(<HeatmapList>)
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Draw the List of Heatmaps |
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draw_title(<Heatmap>)
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Draw Heatmap Title |
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draw_title(<HeatmapList>)
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Draw Heatmap List Title |
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draw_title-dispatch
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Method dispatch page for draw_title |
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extract_comb()
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Extract Elements in a Combination set |
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getXY_in_parent_vp()
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Convert XY in a Parent Viewport |
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get_color_mapping_list(<HeatmapAnnotation>)
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Get a List of ColorMapping objects |
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get_legend_param_list(<HeatmapAnnotation>)
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Get a List of Annotation Legend Parameters |
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grid.annotation_axis()
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Draw Annotation Axis |
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grid.boxplot()
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Draw a Single Boxplot |
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grid.dendrogram()
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Draw the Dendrogram |
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grid.draw(<Legends>)
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Draw the Legends |
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heatmap_legend_size(<HeatmapList>)
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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>)
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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>)
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Height of the Heatmap List |
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height(<Legends>)
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Height of the Legends |
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height(<SingleAnnotation>)
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Height of the SingleAnnotation object |
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`height<-`(<AnnotationFunction>)
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Assign the Height to the AnnotationFunction Object |
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`height<-`(<HeatmapAnnotation>)
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Assign the Height to the HeatmapAnnotation Object |
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`height<-`(<SingleAnnotation>)
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Assign the Height to the SingleAnnotation Object |
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heightDetails(<annotation_axis>)
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Height for annotation_axis Grob |
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heightDetails(<legend>)
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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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ht_global_opt()
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Global Options for Heatmaps |
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ht_opt()
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Global Options for Heatmaps |
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is_abs_unit()
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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>)
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Length of the HeatmapList object |
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list_components()
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List All Heatmap Components |
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list_to_matrix()
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Convert a List of Sets to a Binary Matrix |
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make_column_cluster(<Heatmap>)
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Make Cluster on Columns |
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make_comb_mat()
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Make a Combination Matrix for UpSet Plot |
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make_layout(<Heatmap>)
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Make the Layout of a Single Heatmap |
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make_layout(<HeatmapList>)
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Make Layout for the Heatmap List |
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make_layout-dispatch
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Method dispatch page for make_layout |
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make_row_cluster(<Heatmap>)
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Make Cluster on Rows |
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map_to_colors(<ColorMapping>)
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Map Values to Colors |
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max_text_height()
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Maximum Height of Text |
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max_text_width()
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Maximum Width of Text |
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merge_dendrogram()
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Merge Dendrograms |
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names(<HeatmapAnnotation>)
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Annotation Names |
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names(<HeatmapList>)
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Names of the heatmaps/annotations |
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`names<-`(<HeatmapAnnotation>)
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Assign Annotation Names |
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ncol(<Heatmap>)
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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>)
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Number of Observations |
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normalize_comb_mat()
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Normalize a list of combination matrice |
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nrow(<Heatmap>)
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Number of Rows in the Heatmap |
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oncoPrint()
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Make oncoPrint |
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order.comb_mat()
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Order of the Combination Sets |
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packLegend()
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Pack Legends |
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`%v%`
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Vertically Add Heatmaps or Annotations to a Heatmap List |
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pindex()
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Get Values in a Matrix by Pair-wise Indices |
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prepare(<Heatmap>)
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Prepare the Heatmap |
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print(<comb_mat>)
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Print the comb_mat Object |
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re_size(<HeatmapAnnotation>)
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Resize the Width or Height of Heatmap Annotations |
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restore_matrix()
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Restore the index vector to index matrix in layer_fun |
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rowAnnotation()
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Construct Row Annotations |
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row_anno_barplot()
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Barplots as Row Annotation |
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row_anno_boxplot()
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Boxplots as Row Annotation |
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row_anno_density()
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Density as Row Annotation |
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row_anno_histogram()
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Histograms as Row Annotation |
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row_anno_link()
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Label Markers as Row Annotation |
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row_anno_points()
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Points as Row Annotation |
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row_anno_text()
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Text as Row Annotation |
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row_dend(<Heatmap>)
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Get Row Dendrograms from a Heatmap |
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row_dend(<HeatmapList>)
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Get Row Dendrograms from a Heatmap List |
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row_dend-dispatch
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Method dispatch page for row_dend |
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row_order(<Heatmap>)
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Get Row Order from a Heatmap |
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row_order(<HeatmapList>)
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Get Row Order from a Heatmap List |
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row_order-dispatch
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Method dispatch page for row_order |
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set_component_height(<Heatmap>)
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Set Height of Heatmap Component |
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set_component_width(<Heatmap>)
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Set Width of Heatmap Component |
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set_name()
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Set Names |
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set_size()
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Set Sizes |
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show(<AnnotationFunction>)
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Print the AnnotationFunction Object |
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show(<ColorMapping>)
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Print the ColorMapping Object |
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show(<Heatmap>)
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Draw the Single Heatmap with Defaults |
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show(<HeatmapAnnotation>)
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Print the HeatmapAnnotation object |
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show(<HeatmapList>)
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Draw a list of heatmaps with default parameters |
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show(<SingleAnnotation>)
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Print the SingleAnnotation object |
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show-dispatch
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Method dispatch page for show |
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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>)
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Size of the SingleAnnotation Object |
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`size<-`(<AnnotationFunction>)
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Assign the Size to the AnnotationFunction Object |
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`size<-`(<HeatmapAnnotation>)
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Assign the Size to the HeatmapAnnotation Object |
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`size<-`(<SingleAnnotation>)
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Assign the Size to the SingleAnnotation Object |
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smartAlign2()
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Adjust positions of rectanglar shapes |
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str(<comb_mat>)
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str method |
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subset_gp()
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Subset a gpar Object |
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subset_matrix_by_row()
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Subset the Matrix by Rows |
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subset_vector()
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Subset the vector |
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summary(<Heatmap>)
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Print the Summary of a Heatmap |
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summary(<HeatmapList>)
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Summary of a Heatmap List |
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t(<comb_mat>)
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Transpost the Combination Matrix |
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test_alter_fun()
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Test alter_fun for oncoPrint() |
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unify_mat_list()
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Unify a List of Matrix |
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upset_right_annotation()
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Default UpSet Right Annotation |
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upset_top_annotation()
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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>)
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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>)
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Width of the Heatmap List |
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width(<Legends>)
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Width of the Legends |
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width(<SingleAnnotation>)
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Width of the SingleAnnotation Object |
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`width<-`(<AnnotationFunction>)
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Assign the Width to the AnnotationFunction Object |
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`width<-`(<HeatmapAnnotation>)
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Assign the Width to the HeatmapAnnotation Object |
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`width<-`(<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>)
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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 |