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

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

Helper to specify heatmap annotation for variable distribution density plot

Description

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

Usage

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"
  )
)

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