Functional-marker positivity figure — fig_functional

Delegates to fig_group_comparison(), exactly as fig_population_frequencies() does, so a monocyte HLA-DR shift gets the same bar/median/whisker/points treatment and the same Wilcoxon brackets as a population-abundance shift – before this figure existed, functional_markers.csv was written but never plotted, so a functional difference between cohorts was visible only as rows in a CSV.

Usage

fig_functional_markers(
  fx,
  outfile,
  group_of = NULL,
  stats = NULL,
  reference = NULL,
  p_source = c("raw", "BH"),
  ncol = 3L,
  panel_label = "",
  dpi = 300,
  colors = fcs_colors(),
  group_noun = "group"
)

Arguments

fx: functional_markers table (sample_id, block, population, marker, pct_positive, is_control). Population x marker becomes the panel key, because a positivity threshold only means something inside the population it was derived for.
outfile: Path to write the figure to.
group_of: optional sample_id -> group map; NULL pools every sample into "All samples" (mirrors fig_population_frequencies()).
stats: Statistics table from the matching stats_ function, used to annotate the figure.
reference: The group every other group is compared against.
p_source: Which p-value the figure annotates: raw or BH-adjusted. Default c("raw", "BH").
ncol: Number of panel columns; NULL computes one that keeps the canvas roughly square. Default 3L.
panel_label: Marker-panel name added to the figure title; empty for none. Default "".
dpi: Resolution in dots per inch. May be reduced automatically to respect the raster ceiling; see safe_ggsave(). Default 300.
colors: Named list of colours; defaults to the package palette. See fcs_colors(). Default fcs_colors().
group_noun: what the groups are, completing the title; see fig_group_comparison().