Initial reconnaissance / QC diagnostic figure – run on EVERY batch

WHAT: a three-row diagnostic across all input files: row 1 log10 FSC-A vs log10 SSC-A occupancy with the derived leukocyte gate row 2 CD45 (asinh) vs log10 SSC-A with the derived CD45 cutoff row 3 overlaid density of the lineage markers within the CD45+ parent WHY: this is the figure that catches the three failure modes that silently ruin a run: (a) gating debris instead of leukocytes – visible as a dense low-FSC blob sitting at CD45 background, (b) a mis-placed CD45 cutoff, and (c) unstained or failed-staining files, visible as marker densities collapsed into a single background peak. It must be inspected before any downstream result is trusted.

Usage

fig_recon_diagnostics(
  recon,
  outfile,
  max_points = 40000L,
  dpi = 300,
  dens_markers = NULL,
  colors = fcs_colors(),
  scale_label = "asinh intensity"
)

Arguments

recon: list of per-file diagnostic records, each a list with: sample_id, panel, fsc_log10, ssc_log10 (numeric vectors, may be subsampled), cd45 (asinh vector or NULL), gate (list with fsc_lo/fsc_hi/ssc_lo/ssc_hi), cd45_threshold (numeric or NA), marker_densities (named list of asinh vectors within the CD45+ parent), verdict (character, from staining QC).
outfile: Path to write the figure to.
max_points: The max points. Default 40000L.
dpi: Resolution in dots per inch. May be reduced automatically to respect the raster ceiling; see safe_ggsave(). Default 300.
dens_markers: The dens markers.
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".

Value

the composed patchwork object (also written to outfile).