anno_block: Block annotation

In jokergoo/ComplexHeatmap: Make Complex Heatmaps

Block annotation

Description

Block annotation

Usage

anno_block(align_to = NULL, gp = gpar(), labels = NULL, labels_gp = gpar(),
    labels_rot = ifelse(which == "row", 90, 0),
    labels_offset = unit(0.5, "npc"), labels_just = "center",
    which = c("column", "row"), width = NULL, height = NULL, show_name = FALSE,
    panel_fun = NULL)

Arguments

align_to	If you don't want to create block annotation for all slices, you can specify a list of indices that cover continuously adjacent rows or columns.
gp	Graphic parameters.
labels	Labels put on blocks.
labels_gp	Graphic parameters for labels.
labels_rot	Rotation for labels.
labels_offset	Positions of the labels. It controls offset on y-directions for column annotation and on x-directoin for row annotation.
labels_just	Jusification of the labels.
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.
show_name	Whether show annotatio name.
panel_fun	A self-defined function that draws graphics in each slice. It must have two arguments: 1. row/column indices for the current slice and 2. a vector of levels from the split variable that correspond to current slice. When graphics is set, all other graphics parameters in anno_block are ignored.

Details

The block annotation is used for representing slices. The length of all arguments should be 1 or the number of slices.

Value

An annotation function which can be used in HeatmapAnnotation.

See Also

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

Examples

Heatmap(matrix(rnorm(100), 10), 
    top_annotation = HeatmapAnnotation(foo = anno_block(gp = gpar(fill = 2:4),
        labels = c("group1", "group2", "group3"), labels_gp = gpar(col = "white"))),
    column_km = 3,
    left_annotation = rowAnnotation(foo = anno_block(gp = gpar(fill = 2:4),
        labels = c("group1", "group2", "group3"), labels_gp = gpar(col = "white"))),
    row_km = 3)

# =============  set the panel_fun argument ==============
col = c("1" = "red", "2" = "blue", "A" = "green", "B" = "orange")
Heatmap(matrix(rnorm(100), 10), row_km = 2, row_split = sample(c("A", "B"), 10, replace = TRUE)) + 
rowAnnotation(foo = anno_block(
	panel_fun = function(index, levels) {
		grid.rect(gp = gpar(fill = col[levels[2]], col = "black"))
		grid.text(paste(levels, collapse = ","), 0.5, 0.5, rot = 90,
			gp = gpar(col = col[levels[1]]))
	}
))

labels = c("1" = "one", "2" = "two", "A" = "Group_A", "B" = "Group_B")
Heatmap(matrix(rnorm(100), 10), row_km = 2, row_split = sample(c("A", "B"), 10, replace = TRUE)) + 
rowAnnotation(foo = anno_block(panel_fun = function(index, levels) {
	grid.rect(gp = gpar(fill = col[levels[2]], col = "black"))
	grid.text(paste(labels[levels], collapse = ","), 0.5, 0.5, rot = 90,
		gp = gpar(col = col[levels[1]]))
}))

Heatmap(matrix(rnorm(100), 10), row_km = 2, row_split = sample(c("A", "B"), 10, replace = TRUE)) + 
rowAnnotation(foo = anno_block(
	panel_fun = function(index, levels) {
		grid.rect(gp = gpar(fill = col[levels[2]], col = "black"))
		txt = paste(levels, collapse = ",")
		txt = paste0(txt, "\n", length(index), " rows")
		grid.text(txt, 0.5, 0.5, rot = 0,
			gp = gpar(col = col[levels[1]]))
	},
	width = unit(3, "cm")
))

# =========== set align_to ################
col = c("foo" = "red", "bar" = "blue")
Heatmap(matrix(rnorm(100), 10), cluster_rows = FALSE) +
rowAnnotation(foo = anno_block(
	align_to = list(foo = 1:4, bar = 6:10),
	panel_fun = function(index, nm) {
		grid.rect(gp = gpar(fill = col[nm]))
		grid.text(nm, 0.5, 0.5)
	},
	width = unit(2, "cm"))
)

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