anno_tax_density: Helper to specify heatmap annotation for showing taxa...

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

Helper to specify heatmap annotation for showing taxa abundance density plot

Description

Use this as an argument to taxAnnotation(), which itself is used by cor_heatmap and comp_heatmap as tax_anno argument.

Usage

anno_tax_density(
  undetected = 0,
  only_detected = TRUE,
  trans = "log10p",
  zero_replace = 0,
  use_counts = TRUE,
  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,
  taxa = NULL,
  which = NULL
)

Arguments

undetected	the value above which taxa are classed as detected/present in a sample
only_detected	only plot values for samples where the taxon abundance is > undetected
trans	name of transformation suitable for tax_transform, or a function calling tax_transform, and/or tax_scale, (a function must take a phyloseq or psExtra, and return one)
zero_replace	zero_replace value for for tax_transform, ignored if trans is a function
use_counts	try to retrieve counts from data object?
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
taxa	OPTIONAL selection vector of taxa (names, numbers or logical), 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")
data("ibd", package = "microViz")
psq <- tax_filter(ibd, min_prevalence = 5)
psq <- tax_mutate(psq, Species = NULL)
psq <- tax_fix(psq)
psq <- tax_agg(psq, rank = "Family")
taxa <- tax_top(psq, n = 15, rank = "Family")
# makes a function that takes data, taxa and which (at minimum)
fun <- anno_tax_density()
# manually specify the density plot function by giving it data etc.
heatmapAnnoFunction <- fun(data = psq, which = "column", taxa = taxa)

# draw the density plot without a heatmap, you will never normally do this!
vp <- viewport(width = 0.75, height = 0.75)
grid.newpage()
pushViewport(vp)
draw(heatmapAnnoFunction)

# let's change some style options and specify the data up front
grid.newpage()
pushViewport(vp)
draw(anno_tax_density(
  data = psq, taxa = taxa, which = "row",
  gp = grid::gpar(fill = "red"), border = FALSE
))

# heatmap type, with alternative transformation and axis_param
grid.newpage()
pushViewport(vp)
draw(anno_tax_density(
  data = psq, taxa = taxa, which = "row", type = "heatmap",
  trans = "log2", zero_replace = "halfmin", axis_param = list(labels_rot = 0)
))

grid.newpage()

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