anno_zoom: Zoom annotation

In jokergoo/ComplexHeatmap: Make Complex Heatmaps

Zoom annotation

Description

Zoom annotation

Usage

anno_zoom(align_to, panel_fun = function(index, nm = NULL) { grid.rect() },
    which = c("column", "row"), side = ifelse(which == "column", "top", "right"),
    size = NULL, gap = unit(1, "mm"),
    link_width = unit(5, "mm"), link_height = link_width, link_gp = gpar(),
    extend = unit(0, "mm"), width = NULL, height = NULL, internal_line = TRUE)

Arguments

align_to	It defines how the boxes correspond to the rows or the columns in the heatmap. If the value is a list of indices, each box corresponds to the rows or columns with indices in one vector in the list. If the value is a categorical variable (e.g. a factor or a character vector) that has the same length as the rows or columns in the heatmap, each box corresponds to the rows/columns in each level in the categorical variable.
panel_fun	A self-defined function that defines how to draw graphics in the box. The function must have a index argument which is the indices for the rows/columns that the box corresponds to. It can have second argument nm which is the "name" of the selected part in the heatmap. The corresponding value for nm comes from align_to if it is specified as a categorical variable or a list with names.
which	Whether it is a column annotation or a row annotation?
side	Side of the boxes If it is a column annotation, valid values are "top" and "bottom"; If it is a row annotation, valid values are "left" and "right".
size	The size of boxes. It can be pure numeric that they are treated as relative fractions of the total height/width of the heatmap. The value of size can also be absolute units.
gap	Gaps between boxes.
link_gp	Graphic settings for the segments.
link_width	Width of the segments.
link_height	Similar as link_width, used for column annotation.
extend	By default, the region for the labels has the same width (if it is a column annotation) or same height (if it is a row annotation) as the heatmap. The size can be extended by this options. The value can be a proportion number or a unit object. The length can be either one or two.
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.
internal_line	Internally used.

Details

anno_zoom creates several plotting regions (boxes) which can be corresponded to subsets of rows/columns in the heatmap.

Value

An annotation function which can be used in HeatmapAnnotation.

See Also

https://jokergoo.github.io/ComplexHeatmap-reference/book/heatmap-annotations.html#zoom-annotation

Examples

set.seed(123)
m = matrix(rnorm(100*10), nrow = 100)
subgroup = sample(letters[1:3], 100, replace = TRUE, prob = c(1, 5, 10))
rg = range(m)
panel_fun = function(index, nm) {
	pushViewport(viewport(xscale = rg, yscale = c(0, 2)))
	grid.rect()
	grid.xaxis(gp = gpar(fontsize = 8))
	grid.boxplot(m[index, ], pos = 1, direction = "horizontal")
	grid.text(paste("distribution of group", nm), mean(rg), y = 1.9, 
		just = "top", default.units = "native", gp = gpar(fontsize = 10))
	popViewport()
}
anno = anno_zoom(align_to = subgroup, which = "row", panel_fun = panel_fun, 
	size = unit(2, "cm"), gap = unit(1, "cm"), width = unit(4, "cm"))
Heatmap(m, right_annotation = rowAnnotation(foo = anno), row_split = subgroup)

jokergoo/ComplexHeatmap documentation built on Dec. 22, 2024, 8:51 a.m.