Per-sample (or per-group) density comparison over the shared embedding

WHY: side-by-side 2D density of the SAME embedding shows where each sample or group gains or loses cells – the comparison the shared embedding exists for. Called with facet_by = "sample_id" (the default) for per-sample QC, and again with the resolved group column when 2+ groups exist, so cohorts can be compared the same way sample_id already is.

Usage

fig_density_by_sample(
  cells,
  outfile,
  panel_label = "",
  facet_by = "sample_id",
  dpi = 300,
  colors = fcs_colors()
)

Arguments

cells

Embedded cell table: one row per cell, carrying umap_1/umap_2, sample_id, population_label and one column per marker.

outfile

Path to write the figure to.

panel_label

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

facet_by

any column present in cells – sample_id, cohort, or any other covariate the patient table carried through.

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().