Event rate across the acquisition, with the flagged intervals marked

One panel per sample. The line is how many events the instrument recorded in each equal-width slice of the acquisition, and the marked points are the slices whose rate or whose channel medians departed from the rest of that file.

Usage

fig_acquisition_qc(
  bins,
  outfile,
  summary = NULL,
  dpi = 200,
  colors = fcs_colors()
)

Arguments

bins

the bins element of run_acquisition_qc()

outfile

Path to write the figure to.

summary

the summary element, used for the subtitle

dpi

Resolution in dots per inch. Default 200.

colors

Named list of colours; defaults to the package palette. Default fcs_colors().

Details

WHAT TO LOOK FOR. A clean acquisition is a roughly flat line: the instrument delivered cells at a steady rate and the signal did not move. A sustained trough is a partial clog. A spike is usually a bubble or a sample that was disturbed. A step is a settings change part-way through the tube.

WHY THE RATE AND NOT THE SIGNAL IS PLOTTED. Both are tested, and the flag on each point reflects whichever failed, but the rate is the one quantity that is on a single comparable axis for every panel and every instrument. The channel that drove each flag is named in acquisition_qc.csv rather than drawn here, because one panel per sample per channel is not a figure anyone reads.