Helper to specify heatmap annotation for variable distribution density plot

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

anno_var_density(
  fun = identity,
  size = grid::unit(30, "mm"),
  type = c("lines", "violin", "heatmap"),
  xlim = NULL,
  heatmap_colors = c("white", "forestgreen"),
  joyplot_scale = 1.5,
  border = TRUE,
  gp = grid::gpar(fill = "lightgrey"),
  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

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.

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?

...

Arguments passed on to ComplexHeatmap::anno_density

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


grid.newpage()
pushViewport(vp)
draw(
  anno_var_density(
    data = fakeData, fun = function(x) log(x + 1),
    vars = rev(names(fakeData)), type = "heatmap",
    which = "column"
  )
)