ht_opt {ComplexHeatmap} | R Documentation

## Global Options for Heatmaps

### Description

Global Options for Heatmaps

### Usage

    ht_opt(..., RESET = FALSE, READ.ONLY = NULL, LOCAL = FALSE, ADD = FALSE)

### Arguments

`...` | Options, see 'Details' section.
`RESET` | Reset all the option values.
`READ.ONLY` | Please ignore this argument.
`LOCAL` | Please ignore this argument.
`ADD` | Please ignore this argument.

### Details

You can set some parameters for all heatmaps/annotations simultaneously by this global function. Pleast note you should put it before your heatmap code and reset all option values after drawing the heatmaps to get rid of affecting next heatmap.

There are following parameters to control all heatmaps:

heatmap_row_names_gp

  set `row_names_gp` in all `Heatmap`.

heatmap_column_names_gp

  set `column_names_gp` in all `Heatmap`.

heatmap_row_title_gp

  set `row_title_gp` in all `Heatmap`.

heatmap_column_title_gp

  set `column_title_gp` in all `Heatmap`.

heatmap_border

  set `border` in all `Heatmap`.

Following parameters control the legends:

legend_title_gp

  set `title_gp` in all heatmap legends and annotation legends.

legend_title_position

  set `title_position` in all heatmap legends and annotation legends.

legend_labels_gp

  set `labels_gp` in all heatmap legends and annotation legends.

legend_grid_width

  set `grid_width` in all heatmap legends and annotation legends.

legend_grid_height

  set `grid_height` in all heatmap legends and annotation legends.

legend_border

  set `border` in all heatmap legends and annotation legends.

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.

Following parameters control heatmap annotations:

annotation_border

  `border` in all `HeatmapAnnotation`.

simple_anno_size

  size for the simple annotation.

Following parameters control the space between heatmap components:

DENDROGRAM_PADDING

  space bewteen dendrograms and heatmap body.

DIMNAME_PADDING

  space between row/column names and heatmap body.

TITLE_PADDING

  space between row/column titles and heatmap body.

COLUMN_ANNO_PADDING

  space between column annotations and heatmap body.

ROW_ANNO_PADDING

  space between row annotations and heatmap body.

HEATMAP_LEGEND_PADDING

  space between heatmap legends and heatmaps

ANNOTATION_LEGEND_PADDING

  space between annotation legends and heatmaps

Other parameters:

fast_hclust

  whether use `hclust` to speed up clustering?

show_parent_dend_line

  when heatmap is split, whether to add a dashed line to mark parent dendrogram and children dendrograms?

You can get or set option values by the traditional way (like `options`) or by `$` operator:

        # to get option values
        ht_opt("heatmap_row_names_gp")
        ht_opt$heatmap_row_names_gp

        # to set option values
        ht_opt("heatmap_row_names_gp" = gpar(fontsize = 8))
        ht_opt$heatmap_row_names_gp = gpar(fontsize = 8)

Reset to the default values by `ht_opt(RESET = TRUE)`.

### Author(s)

Zuguang Gu <z.gu@dkfz.de>

### Examples

    ht_opt

[Package ComplexHeatmap version 2.3.4 Index]