make_layout-HeatmapList-method: Make layout for the complete plot

Description Usage Arguments Details Value Author(s) Examples

Description

Make layout for the complete plot

Usage

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## 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(),
    gap = unit(3, "mm"),
    main_heatmap = which(sapply(object@ht_list, inherits, "Heatmap"))[1],
    row_dend_side = c("original", "left", "right"),
    row_hclust_side = row_dend_side,
    row_sub_title_side = c("original", "left", "right"),
    cluster_rows = 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,
    combined_name_fun = 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.

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 of the heatmap legend.

merge_legends

whether put heatmap legends and annotation legends in a same column

show_heatmap_legend

whether show heatmap legend.

heatmap_legend_list

a list of self-defined legend, should be wrapped into grob objects.

annotation_legend_side

side of annotation legend.

show_annotation_legend

whether show annotation legend.

annotation_legend_list

a list of self-defined legend, should be wrapped into grob objects.

gap

gap between heatmaps, should be a unit object.

main_heatmap

name or index for the main heatmap

row_dend_side

if auto adjust, where to put the row dendrograms for the main heatmap

row_hclust_side

deprecated, use row_dend_side instead

row_sub_title_side

if auto adjust, where to put sub row titles for the main heatmap

cluster_rows

same setting as in Heatmap, if it is specified, cluster_rows in main heatmap is ignored.

clustering_distance_rows

same setting as in Heatmap, if it is specified, clustering_distance_rows in main heatmap is ignored.

clustering_method_rows

same setting as in Heatmap, if it is specified, clustering_method_rows in main heatmap is ignored.

row_dend_width

same setting as in Heatmap, if it is specified, row_dend_width in main heatmap is ignored.

show_row_dend

same setting as in Heatmap, if it is specified, show_row_dend in main heatmap is ignored.

row_dend_reorder

same setting as in Heatmap, if it is specified, row_dend_reorder in main heatmap is ignored.

row_dend_gp

same setting as in Heatmap, if it is specified, row_dend_gp in main heatmap is ignored.

row_order

same setting as in Heatmap, if it is specified, row_order in main heatmap is ignored.

km

same setting as in Heatmap, if it is specified, km in main heatmap is ignored.

split

same setting as in Heatmap, if it is specified, split in main heatmap is ignored.

combined_name_fun

same setting as in Heatmap, if it is specified, combined_name_fun in main heatmap is ignored.

Details

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

The layout for the heatmap list and layout for each heatmap are calculated when drawing the heatmap list.

This function is only for internal use.

Value

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

Author(s)

Zuguang Gu <[email protected]>

Examples

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# no example for this internal method
NULL

eilslabs/ComplexHeatmap documentation built on Oct. 19, 2017, 2:13 p.m.