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Last data update: 2014.03.03

R: Draw a list of heatmaps

draw-HeatmapList-method

R Documentation

Draw a list of heatmaps

Description

Draw a list of heatmaps

Usage

## S4 method for signature 'HeatmapList'
draw(object,
    padding = unit(c(2, 2, 2, 2), "mm"),
    newpage = TRUE,
    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"),
    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_sub_title_side = c("original", "left", "right"), ...)

Arguments

`object`	a `HeatmapList-class` object
`padding`	padding of the plot. Elements correspond to bottom, left, top, right paddings.
`newpage`	whether create a new page for the graphics.
`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.
`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_sub_title_side`	if auto adjust, where to put sub row titles for the main heatmap
`...`	pass to `make_layout,HeatmapList-method`

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 list of row dendrograms and column dendrogram.

Author(s)

Zuguang Gu <z.gu@dkfz.de>

Examples

mat = matrix(rnorm(80, 2), 8, 10)
mat = rbind(mat, matrix(rnorm(40, -2), 4, 10))
rownames(mat) = letters[1:12]
colnames(mat) = letters[1:10]

ht = Heatmap(mat)
ht_list = ht + ht
draw(ht_list)
draw(ht_list, row_title = "row title", column_title = "column title", 
	heatmap_legend_side = "top")

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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> library(ComplexHeatmap)
Loading required package: grid
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/ComplexHeatmap/draw-HeatmapList-method.rd_%03d_medium.png", width=480, height=480)
> ### Name: draw-HeatmapList-method
> ### Title: Draw a list of heatmaps
> ### Aliases: draw,HeatmapList-method
> 
> ### ** Examples
> 
> mat = matrix(rnorm(80, 2), 8, 10)
> mat = rbind(mat, matrix(rnorm(40, -2), 4, 10))
> rownames(mat) = letters[1:12]
> colnames(mat) = letters[1:10]
> 
> ht = Heatmap(mat)
> ht_list = ht + ht
Warning message:
In .local(object, ...) :
  Heatmap/row annotaiton names are duplicated: matrix_1
> draw(ht_list)
> draw(ht_list, row_title = "row title", column_title = "column title", 
+ 	heatmap_legend_side = "top")
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>