Man pages for ComplexHeatmap
Make Complex Heatmaps

add.AdditiveUnitHorizontally Add Heatmaps or Annotations to a Heatmap List
add_heatmap-dispatchMethod dispatch page for add_heatmap
add_heatmap-HeatmapAnnotation-methodAdd Annotations or Heatmaps as a Heatmap List
add_heatmap-HeatmapList-methodAdd heatmaps and row annotations to the heatmap list
add_heatmap-Heatmap-methodAdd Heatmap to the Heatmap List
AdditiveUnitConstructor Method for AdditiveUnit Class
AdditiveUnit-classClass for Concatenating Heatmaps and Annotations
adjust_dend_by_xAdjust the Positions of nodes/leaves in the Dendrogram
adjust_heatmap_list-HeatmapList-methodAdjust Heatmap List
alter_graphicAutomatically generate alter_fun
anno_barplotBarplot Annotation
anno_blockBlock annotation
anno_boxplotBoxplot Annotation
anno_densityDensity Annotation
anno_emptyEmpty Annotation
anno_histogramHistogram Annotation
anno_horizonHorizon chart Annotation
anno_imageImage Annotation
anno_joyplotJoyplot Annotation
anno_linesLines Annotation
anno_linkLink Annotation
anno_markLink annotation with labels
anno_oncoprint_barplotBarplot Annotation for oncoPrint
anno_pointsPoints Annotation
anno_simpleSimple Annotation
anno_summarySummary Annotation
annotation_axis_grobGrob for Annotation Axis
AnnotationFunctionConstructor of AnnotationFunction Class
AnnotationFunction-classThe AnnotationFunction Class
annotation_legend_size-HeatmapList-methodSize of the Annotation Legends
anno_textText Annotation
anno_zoomZoom annotation
attach_annotation-Heatmap-methodAttach heatmap annotations to the heatmap
c.ColorMappingConcatenate A List of ColorMapping objects
c.HeatmapAnnotationConcatenate Heatmap Annotations
cluster_within_groupCluster within and between Groups
ColorMappingConstructor Method for ColorMapping Class
ColorMapping-classClass for Color Mapping
color_mapping_legend-ColorMapping-methodDraw Legend Based on Color Mapping
columnAnnotationConstruct Column Annotations
column_dend-dispatchMethod dispatch page for column_dend
column_dend-HeatmapList-methodGet Column Dendrograms from a hHeatmap List
column_dend-Heatmap-methodGet Column Dendrograms from a Heatmap
column_order-dispatchMethod dispatch page for column_order
column_order-HeatmapList-methodGet Column Order from a Heatmap List
column_order-Heatmap-methodGet Column Order from a Aeatmap List
comb_degreeDegrees of the Combination sets
comb_nameNames of the Combination sets
comb_sizeSizes of the Combination sets
compare_pheatmapCompare heatmaps between pheatmap::pheatmap() and...
complement_sizeComplement Set Size
ComplexHeatmap-packageMake complex heatmaps
component_height-dispatchMethod dispatch page for component_height
component_height-HeatmapList-methodHeight of Heatmap List Components
component_height-Heatmap-methodHeights of Heatmap Components
component_width-dispatchMethod dispatch page for component_width
component_width-HeatmapList-methodWidth of Heatmap List Components
component_width-Heatmap-methodWidths of Heatmap Components
copy_all-AnnotationFunction-methodCopy the AnnotationFunction Object
copy_all-dispatchMethod dispatch page for copy_all
copy_all-SingleAnnotation-methodCopy the SingleAnnotation object
decorate_annotationDecorate Heatmap Annotation
decorate_column_dendDecorate Heatmap Column Dendrograms
decorate_column_namesDecorate Heatmap Column Names
decorate_column_titleDecorate Heatmap Column Titles
decorate_dendDecorate Heatmap Dendrograms
decorate_dimnamesDecorate Heatmap Dimension Names
decorate_heatmap_bodyDecorate Heatmap Bodies
decorate_row_dendDecorate Heatmap Row Dendrograms
decorate_row_namesDecorate Heatmap Row Names
decorate_row_titleDecorate Heatmap Row Titles
decorate_titleDecorate Heatmap Titles
default_axis_paramThe Default Parameters for Annotation Axis
default_get_typeDefault get_type for oncoPrint()
dend_heightsHeight of the Dendrograms
dendrogramGrobGrob for Dendrogram
dend_xyCoordinates of the Dendrogram
densityHeatmapVisualize Density Distribution by Heatmap
dim.HeatmapDimension of the Heatmap
dist2Calculate Pairwise Distance from a Matrix
draw-AnnotationFunction-methodDraw the AnnotationFunction Object
draw_annotation-Heatmap-methodDraw Heatmap Annotations on the Heatmap
draw_annotation_legend-HeatmapList-methodDraw legends for All Annotations
draw_dend-Heatmap-methodDraw Heatmap Dendrograms
draw_dimnames-Heatmap-methodDraw row names or column names
draw-dispatchMethod dispatch page for draw
draw-HeatmapAnnotation-methodDraw the Heatmap Annotations
draw_heatmap_body-Heatmap-methodDraw Heatmap Body
draw_heatmap_legend-HeatmapList-methodDraw legends for All Heatmaps
draw_heatmap_list-HeatmapList-methodDraw the List of Heatmaps
draw-HeatmapList-methodDraw a list of heatmaps
draw-Heatmap-methodDraw a Single Heatmap
draw-Legends-methodDraw the Legends
draw-SingleAnnotation-methodDraw the Single Annotation
draw_title-dispatchMethod dispatch page for draw_title
draw_title-HeatmapList-methodDraw Heatmap List Title
draw_title-Heatmap-methodDraw Heatmap Title
Extract.AnnotationFunctionSubset an AnnotationFunction Object
extract_combExtract Elements in a Combination set
Extract.comb_matSubset the Combination Matrix
Extract.gridtextSubset method of gridtext class
Extract.HeatmapSubset a Heatmap
Extract.HeatmapAnnotationSubset the HeatmapAnnotation object
Extract.HeatmapListSubset a HeatmapList object
Extract.SingleAnnotationSubset an SingleAnnotation Object
full_comb_codeFull set of code of combination sets
get_color_mapping_list-HeatmapAnnotation-methodGet a List of ColorMapping objects
get_legend_param_list-HeatmapAnnotation-methodGet a List of Annotation Legend Parameters
getXY_in_parent_vpConvert XY in a Parent Viewport
grid.annotation_axisDraw Annotation Axis
grid.boxplotDraw a Single Boxplot
grid.dendrogramDraw the Dendrogram
grid.draw.LegendsDraw the Legends
gt_renderMark the text for the rendering by gridtext package
HeatmapConstructor method for Heatmap class
HeatmapAnnotationConstructor Method for HeatmapAnnotation class
HeatmapAnnotation-classClass for Heatmap Annotations
Heatmap-classClass for a Single Heatmap
heatmap_legend_size-HeatmapList-methodSize of the Heatmap Legends
HeatmapListConstructor method for HeatmapList class
HeatmapList-classClass for a list of heatmaps
height.AnnotationFunctionHeight of the AnnotationFunction Object
heightAssign.AnnotationFunctionAssign the Height to the AnnotationFunction Object
heightAssign.HeatmapAnnotationAssign the Height to the HeatmapAnnotation Object
heightAssign.SingleAnnotationAssign the Height to the SingleAnnotation Object
heightDetails.annotation_axisHeight for annotation_axis Grob
heightDetails.legendGrob height for packed_legends
heightDetails.legend_bodyGrob height for legend_body
heightDetails.packed_legendsGrob height for packed_legends
height.HeatmapHeight of the Heatmap
height.HeatmapAnnotationHeight of the HeatmapAnnotation Object
height.HeatmapListHeight of the Heatmap List
height.LegendsHeight of the Legends
height.SingleAnnotationHeight of the SingleAnnotation object
ht_global_optGlobal Options for Heatmaps
ht_optGlobal Options for Heatmaps
ht_pos_on_deviceGet the heatmap positions on the graphic device
ht_shinyInteractive heatmaps with a shiny app
ht_sizeCalculate the width and height of the heatmaps
is_abs_unitTest Whether it is an Absolute Unit
LegendMake a Single Legend
LegendsConstructor method for Legends class
Legends-classThe Class for Legends
length.HeatmapAnnotationNumber of Annotations
length.HeatmapListLength of the HeatmapList object
list_componentsList All Heatmap Components
list_to_matrixConvert a List of Sets to a Binary Matrix
make_column_cluster-Heatmap-methodMake Cluster on Columns
make_comb_matMake a Combination Matrix for UpSet Plot
make_layout-dispatchMethod dispatch page for make_layout
make_layout-HeatmapList-methodMake Layout for the Heatmap List
make_layout-Heatmap-methodMake the Layout of a Single Heatmap
make_row_cluster-Heatmap-methodMake Cluster on Rows
map_to_colors-ColorMapping-methodMap Values to Colors
max_text_heightMaximum Height of Text
max_text_widthMaximum Width of Text
merge_dendrogramMerge Dendrograms
namesAssign.HeatmapAnnotationAssign Annotation Names
names.HeatmapAnnotationAnnotation Names
names.HeatmapListNames of the heatmaps/annotations
ncol.HeatmapNumber of Columns in the Heatmap
nobs.AnnotationFunctionNumber of Observations
nobs.HeatmapAnnotationNumber of Observations
nobs.SingleAnnotationNumber of Observations
normalize_comb_matNormalize a list of combination matrice
nrow.HeatmapNumber of Rows in the Heatmap
oncoPrintMake oncoPrint
order.comb_matOrder of the Combination Sets
packLegendPack Legends
pct_v_pctVertically Add Heatmaps or Annotations to a Heatmap List
pheatmapTranslate pheatmap::pheatmap to ComplexHeatmap::Heatmap
pindexGet Values in a Matrix by Pair-wise Indices
prepare-Heatmap-methodPrepare the Heatmap
print.comb_matPrint the comb_mat Object
re_size-HeatmapAnnotation-methodResize the Width or Height of Heatmap Annotations
restore_matrixRestore the index vector to index matrix in layer_fun
row_anno_barplotBarplots as Row Annotation
row_anno_boxplotBoxplots as Row Annotation
row_anno_densityDensity as Row Annotation
row_anno_histogramHistograms as Row Annotation
row_anno_pointsPoints as Row Annotation
rowAnnotationConstruct Row Annotations
row_anno_textText as Row Annotation
row_dend-dispatchMethod dispatch page for row_dend
row_dend-HeatmapList-methodGet Row Dendrograms from a Heatmap List
row_dend-Heatmap-methodGet Row Dendrograms from a Heatmap
row_order-dispatchMethod dispatch page for row_order
row_order-HeatmapList-methodGet Row Order from a Heatmap List
row_order-Heatmap-methodGet Row Order from a Heatmap
selectAreaSelect an area in the heatmap
selectPositionSelect a position in the heatmap
set_component_height-Heatmap-methodSet Height of Heatmap Component
set_component_width-Heatmap-methodSet Width of Heatmap Component
set_nameSet Names
set_nameAssignModify Set Names
set_sizeSet Sizes
show-AnnotationFunction-methodPrint the AnnotationFunction Object
show-ColorMapping-methodPrint the ColorMapping Object
show-dispatchMethod dispatch page for show
show-HeatmapAnnotation-methodPrint the HeatmapAnnotation object
show-HeatmapList-methodDraw a list of heatmaps with default parameters
show-Heatmap-methodDraw the Single Heatmap with Defaults
show-SingleAnnotation-methodPrint the SingleAnnotation object
SingleAnnotationConstructor Method for SingleAnnotation Class
SingleAnnotation-classClass for a Single Annotation
size.AnnotationFunctionSize of the AnnotationFunction Object
sizeAssign.AnnotationFunctionAssign the Size to the AnnotationFunction Object
sizeAssign.HeatmapAnnotationAssign the Size to the HeatmapAnnotation Object
sizeAssign.SingleAnnotationAssign the Size to the SingleAnnotation Object
size.HeatmapAnnotationSize of the HeatmapAnnotation Object
size.SingleAnnotationSize of the SingleAnnotation Object
smartAlign2Adjust positions of rectanglar shapes
str.comb_matstr method
subset_gpSubset a gpar Object
subset_matrix_by_rowSubset the Matrix by Rows
subset_vectorSubset the vector
summary.HeatmapPrint the Summary of a Heatmap
summary.HeatmapListSummary of a Heatmap List
t.comb_matTranspost the Combination Matrix
test_alter_funTest alter_fun for oncoPrint()
unify_mat_listUnify a List of Matrix
UpSetMake the UpSet plot
upset_right_annotationDefault UpSet Right Annotation
upset_top_annotationDefault UpSet Top Annotation
width.AnnotationFunctionWidth of the AnnotationFunction Object
widthAssign.AnnotationFunctionAssign the Width to the AnnotationFunction Object
widthAssign.HeatmapAnnotationAssign the Width to the HeatmapAnnotation Object
widthAssign.SingleAnnotationAssign the Width to the SingleAnnotation Object
widthDetails.annotation_axisWidth for annotation_axis Grob
widthDetails.legendGrob width for packed_legends
widthDetails.legend_bodyGrob width for legend_body
widthDetails.packed_legendsGrob width for packed_legends
width.HeatmapWidth of the Heatmap
width.HeatmapAnnotationWidth of the HeatmapAnnotation Object
width.HeatmapListWidth of the Heatmap List
width.LegendsWidth of the Legends
width.SingleAnnotationWidth of the SingleAnnotation Object
ComplexHeatmap documentation built on Nov. 14, 2020, 2:01 a.m.