anno_barplot: Barplot Annotation
In jokergoo/ComplexHeatmap: Make Complex Heatmaps

View source: R/AnnotationFunction-function.R

anno_barplot

R Documentation

Barplot Annotation

Description

Barplot Annotation

Usage

anno_barplot(x, baseline = 0, which = c("column", "row"), border = TRUE, bar_width = 0.6,
    beside = FALSE, attach = FALSE,
    gp = gpar(fill = "#CCCCCC"), ylim = NULL, extend = 0.05, axis = TRUE,
    axis_param = default_axis_param(which),
    add_numbers = FALSE, numbers_gp = gpar(fontsize = 8),
    numbers_rot = ifelse(which == "column", 45, 0), numbers_offset = unit(2, "mm"),
    width = NULL, height = NULL, ...)

Arguments

`x`	The value vector. The value can be a vector or a matrix. The length of the vector or the number of rows of the matrix is taken as the number of the observations of the annotation. If `x` is a vector, the barplots will be represented as stacked barplots.
`baseline`	baseline of bars. The value should be "min" or "max", or a numeric value. It is enforced to be zero for stacked barplots.
`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.
`beside`	When `x` is a matrix, will bars be positioned beside each other or as stacked bars?
`attach`	When `beside` is `TRUE`, it controls whether bars should be attached.
`gp`	Graphic parameters for bars. The length of each graphic parameter can be 1, length of `x` if `x` is a vector, or number of columns of `x` is `x` is a matrix.
`ylim`	Data ranges. By default it is `range(x)` if `x` is a vector, or `range(rowSums(x))` if `x` is a matrix.
`extend`	The extension to both side of `ylim`. The value is a percent value corresponding to `ylim[2] - ylim[1]`.
`axis`	Whether to add axis?
`axis_param`	parameters for controlling axis. See `default_axis_param` for all possible settings and default parameters.
`add_numbers`	Whether to add numbers to the bars. It only works when `x` is a simple vector.
`numbers_gp`	Graphics parameters for the numbers.
`numbers_rot`	Rotation of numbers.
`numbers_offset`	Offset to the default positions (1mm away the top of the bars).
`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.
`...`	Other arguments.

Value

An annotation function which can be used in HeatmapAnnotation.

Examples

anno = anno_barplot(1:10)
draw(anno, test = "a vector")

m = matrix(runif(4*10), nc = 4)
m = t(apply(m, 1, function(x) x/sum(x)))
anno = anno_barplot(m, gp = gpar(fill = 2:5), bar_width = 1, height = unit(6, "cm"))
draw(anno, test = "proportion matrix")

jokergoo/ComplexHeatmap documentation built on Nov. 17, 2023, 11:27 a.m.