anno_tax_prev: 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 prevalence as barplot

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_prev(
  undetected = 0,
  use_counts = TRUE,
  size = grid::unit(20, "mm"),
  baseline = 0,
  border = TRUE,
  bar_width = 0.6,
  gp = grid::gpar(fill = "#CCCCCC"),
  ylim = NULL,
  extend = 0.05,
  axis = TRUE,
  ...,
  data = NULL,
  taxa = NULL,
  which = NULL
)

Arguments

undetected	the value above which taxa are classed as detected/present in a sample
use_counts	try to retrieve counts from data object?
size	width or height as a grid unit object
baseline	baseline of bars. The value should be "min" or "max", or a numeric value. It is enforced to be zero for stacked barplots.
border	Wether draw borders of the annotation region?
bar_width	Relative width of the bars. The value should be smaller than one.
gp	Graphic parameters for bars. The length of each graphic parameter can be 1, length of x if x is a vector, or number of columns of x is x is a matrix.
ylim	Data ranges. By default it is range(x) if x is a vector, or range(rowSums(x)) if x is a matrix.
extend	The extension to both side of ylim. The value is a percent value corresponding to ylim[2] - ylim[1].
axis	Whether to add axis?
...	Arguments passed on to ComplexHeatmap::anno_barplot 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_prev()

# manually specify the prevalence barplot function by giving it data etc.
heatmapAnnoFunction <- fun(data = psq, which = "row", taxa = taxa)

# draw the barplot without a heatmap, you will never normally do this!
vp <- viewport(width = 0.75, height = 0.75)

grid::grid.newpage()
pushViewport(vp)
draw(heatmapAnnoFunction)

# let's change some style options and specify the data up front
grid::grid.newpage()
pushViewport(vp)
anno_tax_prev(
  data = psq, taxa = taxa, which = "column",
  gp = grid::gpar(fill = "red", lwd = 3, alpha = 0.5),
  border = FALSE, bar_width = 1
) %>%
  draw()

# clear drawings
grid::grid.newpage()

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