Helper to specify comp_heatmap annotation for categorical sample data

Source: R/heatmaps-sampleAnnotation.R

Use this as an argument to sampleAnnotation(), which itself is used by comp_heatmap() as sample_anno argument.

anno_sample_cat(
  var,
  col = distinct_palette(),
  renamer = identity,
  size = grid::unit(5, "mm"),
  legend = TRUE,
  legend_title = "",
  box_col = "white",
  box_lwd = 0.5,
  border_col = NA,
  border_lwd = 1,
  data = NULL,
  samples = NULL,
  which = NULL,
  ...
)

Arguments

var

name of variable to use for annotation data

col

colors vector, at least as long as unique(x), optionally named by x levels

renamer

function to rename levels of variable var

size

width or height as a grid unit object

legend

generate legend for this annotation (attached as attribute of heatmap, and not automatically included in plot)

legend_title

title for legend, if drawn

box_col

colour of boxes around individual cells

box_lwd

line width of boxes around individual cells

border_col

colour of border around all cells

border_lwd

line width of border around all cells

data

OPTIONAL phyloseq or psExtra, only set this to override use of same data as in heatmap

samples

OPTIONAL selection vector of sample 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

...

Arguments passed on to anno_cat

x

data vector, treated as categorical

width

grid unit object or NULL

height

grid unit object or NULL

Value

vector of values

Examples

library("ComplexHeatmap")
data("ibd", package = "microViz")
psq <- ibd
samples <- phyloseq::sample_names(psq)

# makes a function that takes data, taxa and which (at minimum)
fun <- anno_sample_cat(var = "ibd")

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

# 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)
# A legend is attached by default to anno_cat() output, let's plot that.
pushViewport(viewport(x = 0.75))
draw(attr(heatmapAnnoFunction, "Legend"))


# change some options and specify the data up front
grid::grid.newpage()
pushViewport(vp)
anno_sample_cat(
  data = psq, var = "DiseaseState", samples = samples, which = "column",
  size = grid::unit(5, "cm"), col = distinct_palette(pal = "kelly")
) %>%
  draw()