anno_customize: Customized annotation

In jokergoo/ComplexHeatmap: Make Complex Heatmaps

Customized annotation

Description

Customized annotation

Usage

anno_customize(x, graphics = list(), which = c("column", "row"),
    border = TRUE, width = NULL, height = NULL, verbose = TRUE)

Arguments

x	A categorical variable.
graphics	A list of functions that define graphics for each level in x.
which	Is it a row annotation or a column annotation?
width	Width of the annotation. The value should be an absolute unit. Width is not allowed to be set for column annotation.
height	Height of the annotation. The value should be an absolute unit. Height is not allowed to be set for row annotation.
border	Whether to draw border.
verbose	Whether to print messages.

Details

Functions in graphics define simple graphics drawn in each annotation cell. The function takes four arguments:

x,y

Center of the annotation cell.

w,h

Width and height of the annotation cell.

Value

An annotation function which can be used in HeatmapAnnotation.

Examples

x = sort(sample(letters[1:3], 10, replace = TRUE))
graphics = list(
    "a" = function(x, y, w, h) grid.points(x, y, pch = 16),
    "b" = function(x, y, w, h) grid.rect(x, y, w*0.8, h*0.8, gp = gpar(fill = "red")),
    "c" = function(x, y, w, h) grid.segments(x - 0.5*w, y - 0.5*h, x + 0.5*w, y + 0.5*h, gp = gpar(lty = 2))
)

anno = anno_customize(x, graphics = graphics)

m = matrix(rnorm(100), 10)
Heatmap(m, top_annotation = HeatmapAnnotation(bar = x, foo = anno))

# Add legends for `foo`
ht = Heatmap(m, top_annotation = HeatmapAnnotation(bar = x, foo = anno))
lgd = Legend(title = "foo", at = names(graphics), graphics = graphics)
draw(ht, annotation_legend_list = list(lgd))

jokergoo/ComplexHeatmap documentation built on Nov. 17, 2023, 11:27 a.m.