Density Annotation

Density Annotation

anno_density(x, which = c("column", "row"),
    type = c("lines", "violin", "heatmap"),
    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.
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")