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ComplexHeatmap

make_layout-HeatmapList-method

Make Layout for the Heatmap List

Description

Make Layout for the Heatmap List

Usage

## S4 method for signature 'HeatmapList'
make_layout(object,
    
    row_title = character(0),
    row_title_side = c("left", "right"),
    row_title_gp = gpar(fontsize = 14),
    column_title = character(0),
    column_title_side = c("top", "bottom"),
    column_title_gp = gpar(fontsize = 14),
    
    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"),
    
    ht_gap = unit(2, "mm"),
    
    main_heatmap = which(sapply(object@ht_list, inherits, "Heatmap"))[1],
    padding = GLOBAL_PADDING,
    
    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,
    row_km = NULL,
    row_km_repeats = NULL,
    row_split = NULL,
    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)

Arguments

object

A HeatmapList-class object.
row_title

Title on the row.
row_title_side

Will the title be put on the left or right of the heatmap list?
row_title_gp

Graphic parameters for the row title.
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 the column title.
heatmap_legend_side

Side of the heatmap legends.
merge_legends

Whether to put heatmap legends and annotation legends together. By default they are put in different viewports.
show_heatmap_legend

Whether show heatmap legends.
heatmap_legend_list

A list of self-defined legends, should be wrapped into a list of grob objects. Normally they are constructed by Legend.

annotation_legend_side

Side of annotation legends.
show_annotation_legend

Whether show annotation legends.
annotation_legend_list

A list of self-defined legends, should be wrapped into a list of grob objects. Normally they are constructed by Legend.
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".
ht_gap

Gap between heatmaps, should be a unit object. It can be a vector of length 1 or the number of heamtaps/annotations.
main_heatmap

Name or index for the main heatmap.
padding

Padding of the whole plot. The four values correspond to the bottom, left, top and right paddings.
auto_adjust

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

If auto-adjustment is on, to put the row dendrograms of the main heatmap to the most left side of the heatmap list or the most right side?
row_sub_title_side

There can be sub titles generated by the splitting of heatmaps. Similar setting as row_dend_side.
column_dend_side

Similar setting as row_dend_side.
column_sub_title_side

Similar setting as row_sub_title_side.
row_gap

Overwrite the corresponding setting in the main heatmap.
cluster_rows

Overwrite the corresponding setting in the main heatmap.
cluster_row_slices

Overwrite the corresponding setting in the main heatmap.
clustering_distance_rows

Overwrite the corresponding setting in the main heatmap.
clustering_method_rows

Overwrite the corresponding setting in the main heatmap.same setting as in Heatmap, if it is specified, clustering_method_rows in main heatmap is ignored.
row_dend_width

Overwrite the corresponding setting in the main heatmap.
show_row_dend

same Overwrite the corresponding setting in the main heatmap.
row_dend_reorder

Overwrite the corresponding setting in the main heatmap.
row_dend_gp

Overwrite the corresponding setting in the main heatmap.
row_order

Overwrite the corresponding setting in the main heatmap.
row_km

Overwrite the corresponding setting in the main heatmap.
row_km_repeats

Overwrite the corresponding setting in the main heatmap.
row_split

Overwrite the corresponding setting in the main heatmap.
height

Overwrite the corresponding setting in the main heatmap.
heatmap_height

Overwrite the corresponding setting in the main heatmap.
column_gap

Overwrite the corresponding setting in the main heatmap.
cluster_columns

Overwrite the corresponding setting in the main heatmap.
cluster_column_slices

Overwrite the corresponding setting in the main heatmap.
clustering_distance_columns

Overwrite the corresponding setting in the main heatmap.
clustering_method_columns

Overwrite the corresponding setting in the main heatmap.
column_dend_width

column Overwrite the corresponding setting in the main heatmap.
show_column_dend

Overwrite the corresponding setting in the main heatmap.
column_dend_reorder

Overwrite the corresponding setting in the main heatmap.
column_dend_gp

Overwrite the corresponding setting in the main heatmap.
column_order

Overwrite the corresponding setting in the main heatmap.
column_km

Overwrite the corresponding setting in the main heatmap.
column_km_repeats

Overwrite the corresponding setting in the main heatmap.
column_split

Overwrite the corresponding setting in the main heatmap.
width

Overwrite the corresponding setting in the main heatmap.
heatmap_width

Overwrite the corresponding setting in the main heatmap.
use_raster

Overwrite the corresponding setting in every heatmap.
raster_device

Overwrite the corresponding setting in every heatmap.
raster_quality

Overwrite the corresponding setting in every heatmap.
raster_device_param

Overwrite the corresponding setting in every heatmap.
raster_resize

Overwrite the corresponding setting in every heatmap.

Details

It sets the size of each component of the heatmap list and adjusts graphic parameters for each heatmap if necessary.

This function is only for internal use.

Value

A HeatmapList-class object in which settings for all heatmap are adjusted.

Author(s)

Zuguang Gu <z.gu@dkfz.de>

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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