anno_density: Density Annotation

In jokergoo/ComplexHeatmap: Make Complex Heatmaps

Density Annotation

Description

Density Annotation

Usage

anno_density(x, which = c("column", "row"),
    type = c("lines", "violin", "heatmap"), xlim = NULL, max_density = NULL,
    heatmap_colors = rev(brewer.pal(name = "RdYlBu", n = 11)),
    joyplot_scale = 1, border = TRUE, gp = gpar(fill = "#CCCCCC"),
    axis = TRUE, axis_param = default_axis_param(which),
    width = NULL, height = NULL)

Arguments

x	A matrix or a list. If x is a matrix and if which is column, statistics for boxplots are calculated by columns, if which is row, the calculation is done by rows.
which	Whether it is a column annotation or a row annotation?
type	Type of graphics to represent density distribution. "lines" for normal density plot; "violine" for violin plot and "heatmap" for heatmap visualization of density distribution.
xlim	Range on x-axis.
max_density	Maximal density values in the plot. Normally you don't need to manually set it, but when you have multiple density annotations and you want to compare between them, you should manually set this argument to make density distributions are in a same scale.
heatmap_colors	A vector of colors for interpolating density values.
joyplot_scale	Relative height of density distribution. A value higher than 1 increases the height of the density distribution and the plot will represented as so-called "joyplot".
border	Wether draw borders of the annotation region?
gp	Graphic parameters for the boxes. The length of the graphic parameters should be one or the number of observations.
axis	Whether to add axis?
axis_param	parameters for controlling axis. See default_axis_param for all possible settings and default 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.

Value

An annotation function which can be used in HeatmapAnnotation.

See Also

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

Examples

m = matrix(rnorm(100), 10)
anno = anno_density(m, which = "row")
draw(anno, test = "normal density")
anno = anno_density(m, which = "row", type = "violin")
draw(anno, test = "violin")
anno = anno_density(m, which = "row", type = "heatmap")
draw(anno, test = "heatmap")
anno = anno_density(m, which = "row", type = "heatmap", 
    heatmap_colors = c("white", "orange"))
draw(anno, test = "heatmap, colors")

jokergoo/ComplexHeatmap documentation built on Sept. 24, 2024, 4:48 p.m.