ht_opt: Global Options for Heatmaps
In jokergoo/ComplexHeatmap: Make Complex Heatmaps

ht_opt

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.
merge_legend: wether merge heatmap and annotation 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. The value can have length of two which corresponds to the botton and top padding.
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?
COLOR: default colors for continuous color mapping.

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).