Summary Annotation

Summary Annotation

anno_summary(which = c("column", "row"), border = TRUE, bar_width = 0.8,
    axis = TRUE, axis_param = default_axis_param(which),
    ylim = NULL, extend = 0.05, outline = TRUE, box_width = 0.6,
    pch = 1, size = unit(2, "mm"), gp = gpar(),
    width = NULL, height = NULL)

Arguments

which

Whether it is a column annotation or a row annotation?
border

Wether draw borders of the annotation region?
bar_width

Relative width of the bars. The value should be smaller than one.
axis

Whether to add axis?
axis_param

parameters for controlling axis. See default_axis_param for all possible settings and default parameters.
ylim

Data ranges. ylim for barplot is enforced to be c(0, 1).
extend

The extension to both side of ylim. The value is a percent value corresponding to ylim[2] - ylim[1]. This argument is only for boxplot.
outline

Whether draw outline of boxplots?
box_width

Relative width of boxes. The value should be smaller than one.
pch

Point style.
size

Point size.
gp

Graphic parameters.
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.

Details

anno_summary is a special annotation function that it only works for one-column or one-row heatmap. It shows the summary of the values in the heatmap. If the values in the heatmap is discrete, the proportion of each level (the sum is normalized to 1) is visualized as stacked barplot. If the heatmap is split into multiple slices, multiple bars are put in the annotation. If the value is continuous, boxplot is used.

In the barplot, the color schema is used as the same as the heatmap, while for the boxplot, the color needs to be controlled by gp.

Value

An annotation function which can be used in HeatmapAnnotation.

See also

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

Examples

ha = HeatmapAnnotation(summary = anno_summary(height = unit(4, "cm")))
v = sample(letters[1:2], 50, replace = TRUE)
split = sample(letters[1:2], 50, replace = TRUE)
Heatmap(v, top_annotation = ha, width = unit(1, "cm"), split = split)

ha = HeatmapAnnotation(summary = anno_summary(gp = gpar(fill = 2:3), height = unit(4, "cm")))
v = rnorm(50)
Heatmap(v, top_annotation = ha, width = unit(1, "cm"), split = split)