Helper to specify heatmap annotation for variable distribution boxplots

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"
  )
)