Differential-state figure, drawn by the baseline's own comparison figure

WHY IT DELEGATES RATHER THAN DRAWING: fig_group_comparison() already renders exactly this shape – one panel per unit, bar = mean, rule = median, whiskers = SD, points = samples, Wilcoxon brackets. Reusing it means the DS figure cannot drift from the abundance figure's layout, and a reader who has learned to read one has learned to read the other. Exactly the pattern fig_functional_markers() already uses.

Usage

fig_marker_state(
  mfi,
  outfile,
  group_of = NULL,
  stats = NULL,
  reference = NULL,
  p_source = c("raw", "BH"),
  min_cells = 20L,
  ncol = NULL,
  panel_label = "",
  max_panels = 400L,
  dpi = 300,
  colors = fcs_colors(),
  scale_label = "asinh intensity"
)

Arguments

mfi

Per-sample x population x marker summary table.

outfile

Path to write the figure to.

group_of

Named character vector mapping sample_id to group label.

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").

min_cells

Minimum cells a sample must contribute before it is used. Default 20L.

ncol

Number of panel columns; NULL computes one that keeps the canvas roughly square.

panel_label

Marker-panel name added to the figure title; empty for none. Default "".

max_panels

Ceiling on the population x marker panel count. Populations over it are dropped rarest-first – on abundance alone, before any test is consulted, and whole populations rather than individual pairs – and named in the log. Without a bound this figure grows as the product of two independently growing numbers and can exceed what the renderer can build. Default 400L.

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().

scale_label

Name of the scale the intensities are on, the run's transform$label ("asinh intensity", "logicle intensity"). Default "asinh intensity".

Details

WHY pct_positive AND NOT median_asinh IS PLOTTED: fig_group_comparison() fixes the y axis at c(0, headroom) – deliberately, since every quantity it was built for (percentages, concentrations, ratios) is non-negative. Arcsinh medians run negative for dim markers, and handing them to that scale would silently clip the bar to zero and draw a confident-looking panel of a value that is not there. pct_positive is bounded 0 to 100, is a genuine differential-state measure, and is what a bimodal shift moves most. The median_asinh results are not discarded – they carry the full test in the CSV and are the quantity the state heatmap in fig_population_marker_heatmap() draws, where a diverging scale handles sign correctly.