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ComplexHeatmap

draw-HeatmapList-method

Draw a list of heatmaps

Description

Draw a list of heatmaps

Usage

## S4 method for signature 'HeatmapList'
draw(object,
    newpage = TRUE,
    
    row_title = character(0),
    row_title_side = c("left", "right"),
    row_title_gp = gpar(fontsize = 13),
    column_title = character(0),
    column_title_side = c("top", "bottom"),
    column_title_gp = gpar(fontsize = 13),
    
    heatmap_legend_side = c("right", "left", "bottom", "top"),
    merge_legends = FALSE,
    show_heatmap_legend = TRUE,
    heatmap_legend_list = list(),
    annotation_legend_side = c("right", "left", "bottom", "top"),
    show_annotation_legend = TRUE,
    annotation_legend_list = list(),
    align_heatmap_legend = NULL,
    align_annotation_legend = NULL,
    legend_grouping = c("adjusted", "original"),
    
    gap = unit(2, "mm"),
    ht_gap = gap,
    
    main_heatmap = which(sapply(object@ht_list, inherits, "Heatmap"))[1],
    padding = GLOBAL_PADDING,
    adjust_annotation_extension = NULL,
    
    auto_adjust = TRUE,
    row_dend_side = c("original", "left", "right"),
    row_sub_title_side = c("original", "left", "right"),
    column_dend_side = c("original", "top", "bottom"),
    column_sub_title_side = c("original", "top", "bottom"),
    
    row_gap = NULL,
    cluster_rows = NULL,
    cluster_row_slices = NULL,
    clustering_distance_rows = NULL,
    clustering_method_rows = NULL,
    row_dend_width = NULL,
    show_row_dend = NULL,
    row_dend_reorder = NULL,
    row_dend_gp = NULL,
    row_order = NULL,
    km = NULL,
    split = NULL,
    row_km = km,
    row_km_repeats = NULL,
    row_split = split,
    height = NULL,
    heatmap_height = NULL,
    
    column_gap = NULL,
    cluster_columns = NULL,
    cluster_column_slices = NULL,
    clustering_distance_columns = NULL,
    clustering_method_columns = NULL,
    column_dend_width = NULL,
    show_column_dend = NULL,
    column_dend_reorder = NULL,
    column_dend_gp = NULL,
    column_order = NULL,
    column_km = NULL,
    column_km_repeats = NULL,
    column_split = NULL,
    width = NULL,
    heatmap_width = NULL,
    
    use_raster = NULL,
    raster_device = NULL,
    raster_quality = NULL,
    raster_device_param = NULL,
    raster_resize = NULL,
    
    ### global setting
    heatmap_row_names_gp = NULL,
    heatmap_column_names_gp = NULL,
    heatmap_row_title_gp = NULL,
    heatmap_column_title_gp = NULL,
    legend_title_gp = NULL,
    legend_title_position = NULL,
    legend_labels_gp = NULL,
    legend_grid_height = NULL,
    legend_grid_width = NULL,
    legend_border = NULL,
    legend_gap = NULL,
    heatmap_border = NULL,
    annotation_border = NULL,
    fastcluster = NULL,
    simple_anno_size = NULL,
    show_parent_dend_line = NULL)

Arguments

object

a HeatmapList-class object.
newpage

whether create a new page for the graphics. If you want to arrange multiple plots in one page, I suggest to use grid.grabExpr.
row_title

title on the row.
row_title_side

will the title be put on the left or right of the heatmap.
row_title_gp

graphic parameters for drawing text.
column_title

title on the column.
column_title_side

will the title be put on the top or bottom of the heatmap.
column_title_gp

graphic parameters for drawing text.
heatmap_legend_side

side to put heatmap legend
merge_legends

merge heatmap legends and annotation legends to put into one column.
show_heatmap_legend

whether show all heatmap legends
heatmap_legend_list

use-defined legends which are put after the heatmap legends
annotation_legend_side

side of the annotation legends
show_annotation_legend

whether show annotation legends
annotation_legend_list

user-defined legends which are put after the annotation legends
align_heatmap_legend

How to align the legends to heatmap. Possible values are "heatmap_center", "heatmap_top" and "global_center". If the value is NULL, it automatically picks the proper value from the three options.
align_annotation_legend

How to align the legends to heatmap. Possible values are "heatmap_center", "heatmap_top" and "global_center".
legend_grouping

How the legends are grouped. Values should be "adjusted" or "original". If it is set as "original", all annotation legends are grouped together.
gap

gap between heatmaps/annotations
ht_gap

same as gap.
main_heatmap

index of main heatmap. The value can be a numeric index or the heatmap name
padding

padding of the whole plot. The value is a unit vector of length 4, which corresponds to bottom, left, top and right.
adjust_annotation_extension

whether take annotation name into account when calculating positions of graphic elements.
auto_adjust

whether apply automatic adjustment? The auto-adjustment includes turning off dendrograms, titles and row/columns for non-main heatmaps.
row_dend_side

side of the dendrogram from the main heatmap
row_sub_title_side

side of the row title from the main heatmap
column_dend_side

side of the dendrogram from the main heatmap
column_sub_title_side

side of the column title from the main heatmap
row_gap

this modifies row_gap of the main heatmap
cluster_rows

this modifies cluster_rows of the main heatmap
cluster_row_slices

this modifies cluster_row_slices of the main heatmap
clustering_distance_rows

this modifies clustering_distance_rows of the main heatmap
clustering_method_rows

this modifies clustering_method_rows of the main heatmap
row_dend_width

this modifies row_dend_width of the main heatmap
show_row_dend

this modifies show_row_dend of the main heatmap
row_dend_reorder

this modifies row_dend_reorder of the main heatmap
row_dend_gp

this modifies row_dend_gp of the main heatmap
row_order

this modifies row_order of the main heatmap
km

= this modifies km of the main heatmap
split

this modifies split of the main heatmap
row_km

this modifies row_km of the main heatmap
row_km_repeats

this modifies row_km_repeats of the main heatmap
row_split

this modifies row_split of the main heatmap
height

this modifies height of the main heatmap
heatmap_height

this modifies heatmap_height of the main heatmap
column_gap

this modifies column_gap of the main heatmap
cluster_columns

this modifies cluster_columns of the main heatmap
cluster_column_slices

this modifies cluster_column_slices of the main heatmap
clustering_distance_columns

this modifies clustering_distance_columns of the main heatmap
clustering_method_columns

this modifies clustering_method_columns of the main heatmap
column_dend_width

this modifies column_dend_width of the main heatmap
show_column_dend

this modifies show_column_dend of the main heatmap
column_dend_reorder

this modifies column_dend_reorder of the main heatmap
column_dend_gp

this modifies column_dend_gp of the main heatmap
column_order

this modifies column_order of the main heatmap
column_km

this modifies column_km of the main heatmap
column_km_repeats

this modifies column_km_repeats of the main heatmap
column_split

this modifies column_split of the main heatmap
width

this modifies width of the main heatmap
heatmap_width

this modifies heatmap_width of the main heatmap
use_raster

this modifies use_raster of every heatmap.
raster_device

this modifies raster_device of every heatmap.
raster_quality

this modifies raster_quality of every heatmap.
raster_device_param

this modifies raster_device_param of every heatmap.
raster_resize

this modifies raster_resize of every heatmap.
heatmap_row_names_gp

this set the value in ht_opt and reset back after the plot is done
heatmap_column_names_gp

this set the value in ht_opt and reset back after the plot is done
heatmap_row_title_gp

this set the value in ht_opt and reset back after the plot is done
heatmap_column_title_gp

this set the value in ht_opt and reset back after the plot is done
legend_title_gp

this set the value in ht_opt and reset back after the plot is done
legend_title_position

this set the value in ht_opt and reset back after the plot is done
legend_labels_gp

this set the value in ht_opt and reset back after the plot is done
legend_grid_height

this set the value in ht_opt and reset back after the plot is done
legend_grid_width

this set the value in ht_opt and reset back after the plot is done
legend_border

this set the value in ht_opt and reset back after the plot is done
legend_gap

Gap between legends. The value should be a vector of two units. One for gaps between vertical legends and one for the horizontal legends. If only one single unit is specified, the same gap set for the vertical and horizontal legends.

heatmap_border

this set the value in ht_opt and reset back after the plot is done
annotation_border

this set the value in ht_opt and reset back after the plot is done
fastcluster

this set the value in ht_opt and reset back after the plot is done
simple_anno_size

this set the value in ht_opt and reset back after the plot is done
show_parent_dend_line

this set the value in ht_opt and reset back after the plot is done

Details

The function first calls make_layout,HeatmapList-method to calculate the layout of the heatmap list and the layout of every single heatmap, then makes the plot by re-calling the graphic functions which are already recorded in the layout.

Value

This function returns a HeatmapList-class object for which the layout has been created.

Author(s)

Zuguang Gu <z.gu@dkfz.de>

See Also

Examples

# There is no example
NULL
ComplexHeatmap

Make Complex Heatmaps

v2.6.2
MIT + file LICENSE
Authors
Zuguang Gu
Initial release
2020-11-12

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