Population x marker phenotype heatmap

Usage

fig_population_marker_heatmap(
  mfi,
  outfile,
  scale_by = c("marker", "none"),
  min_cells = 20L,
  annotate_expected = NULL,
  panel_label = "",
  dpi = 300,
  colors = fcs_colors(),
  scale_label = "asinh intensity"
)

Arguments

mfi: population_marker_mfi table
outfile: Path to write the figure to.
scale_by: "marker" (row z-score, the annotation/validation view), "none" (raw arcsinh medians, comparable across populations within a marker but not between markers)
min_cells: per-sample floor before a sample contributes to a cell
annotate_expected: optional named list population -> character vector of markers the gate definition REQUIRES to be positive. Drawn as an outline on those cells, turning the figure into an explicit gate audit.
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().
scale_label: Name of the scale the intensities are on, the run's transform$label ("asinh intensity", "logicle intensity"). Default "asinh intensity".