Helper to specify heatmap annotation for showing taxa abundance on boxplot

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

anno_tax_box(
  undetected = 0,
  only_detected = TRUE,
  trans = "compositional",
  zero_replace = 0,
  use_counts = TRUE,
  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,
  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

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

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_box()
# manually specify the prevalence barplot function by giving it data etc.
heatmapAnnoFunction <- fun(data = psq, which = "column", taxa = taxa)
# draw the barplot 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::grid.newpage()
pushViewport(vp)
draw(anno_tax_box(
  data = psq, taxa = taxa, which = "row", pointsize = grid::unit(1, "mm"),
  gp = grid::gpar(fill = "red"), border = FALSE, box_width = 0.2
))


# clear drawings
grid::grid.newpage()