anno_var_box: Helper to specify heatmap annotation for variable...

In david-barnett/microViz: Microbiome Data Analysis and Visualization

Helper to specify heatmap annotation for variable distribution boxplots

Description

Use this as an argument to varAnnotation(), which itself is used by cor_heatmap as var_anno() argument.

Usage

anno_var_box(
  fun = identity,
  size = grid::unit(30, "mm"),
  border = TRUE,
  gp = grid::gpar(fill = "#CCCCCC"),
  ylim = NULL,
  extend = 0.05,
  outline = TRUE,
  box_width = 0.6,
  pch = 1,
  pointsize = grid::unit(0.5, "mm"),
  axis = TRUE,
  ...,
  data = NULL,
  vars = NULL,
  which = NULL
)

Arguments

fun	function applied to all variables, with apply()
size	width or height as a grid unit object
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.
ylim	Data ranges.
extend	The extension to both side of ylim. The value is a percent value corresponding to ylim[2] - ylim[1].
outline	Whether draw outline of boxplots?
box_width	Relative width of boxes. The value should be smaller than one.
pch	Point style.
pointsize	size of outlier points, as grid::unit() object
axis	Whether to add axis?
...	Arguments passed on to ComplexHeatmap::anno_boxplot axis_param parameters for controlling axis. See default_axis_param for all possible settings and default parameters.
data	OPTIONAL phyloseq or psExtra, only set this to override use of same data as in heatmap
vars	OPTIONAL selection vector of variable names, only set this if providing data argument to override default
which	OPTIONAL indicating if it is a 'column' or a 'row' annotation, only set this if providing data argument to override default

Value

function or ComplexHeatmap AnnotationFunction object

Examples

library(ComplexHeatmap)
set.seed(123)
fakeData <- as.data.frame.matrix(matrix(rnorm(500, 10, 3), ncol = 10))
names(fakeData) <- paste0("var_", 1:10)

# draw the boxplot without a heatmap, you will never normally do this!
vp <- viewport(width = 0.75, height = 0.75)
grid.newpage()
pushViewport(vp)
draw(
  anno_var_box(data = fakeData, vars = names(fakeData), which = "column")
)

grid.newpage()
pushViewport(vp)
draw(
  anno_var_box(
    data = fakeData, fun = function(x) log(x + 1),
    vars = rev(names(fakeData)),
    which = "row"
  )
)

david-barnett/microViz documentation built on April 17, 2025, 4:25 a.m.