Benchmark AF Assignment Accuracy Against Spectral Panel Size

Repeatedly subsamples the fluorophore spectra matrix to a range of panel sizes, runs test.af.accuracy for each subsample, and summarises how cosine similarity between raw detector signals and the assigned AF spectra changes with the number of fluorophores. Results are saved as a line-plot PDF and returned as a list.

Usage

benchmark.af.spectra(
  unstained.fcs,
  spectra,
  af.spectra,
  asp,
  functions = c("assign.af.joint.cov", "assign.af.fluorophores", "assign.af.residuals"),
  n.fluors = c(5, 10, 15, 20, 25, 30, 35, 40),
  n.draws = 5L,
  seed = 42L,
  n.downsample = 1000L,
  plot.dir = "figure_af_accuracy",
  filename = "af_accuracy_spectra_benchmark"
)

Arguments

unstained.fcs: Character scalar. Path to the unstained FCS file passed through to test.af.accuracy.
spectra: Numeric matrix of fluorophore spectra (fluorophores x detectors). Row names must be fluorophore names; column names must match the detector channels in the FCS file. Any row named "AF" is removed automatically before processing. Column names must match those of spectra.
af.spectra: Numeric matrix of AF spectra (AF variants x detectors). The first row is treated as the mean AF spectrum and is used for the baseline comparison. Column names must match those of spectra.
asp: Aspect-ratio value passed through to test.af.accuracy.
functions: Character vector of AF-function names to benchmark. See test.af.accuracy for the required calling conventions.
n.fluors: Integer vector of panel sizes (number of fluorophores) to evaluate. Values outside [1, nrow(spectra)] are silently dropped. Default: c(5, 10, 15, 20, 25, 30, 35, 40).
n.draws: Integer scalar. Number of random draws (unique fluorophore subsets) per panel size. A unique seed is derived for each (n.fluors, draw) combination from seed, so results are fully reproducible. Default: 5L.
seed: Integer scalar. Base seed for reproducible subsampling. Default: 42L.
n.downsample: Integer scalar. Maximum number of events passed to each test.af.accuracy call. A random subsample is drawn when the FCS file contains more events. Set to Inf to use all events. Default: 1000L.
plot.dir: Character scalar. Directory for output files. Created recursively if it does not exist. Default: "figure_af_accuracy".
filename: Character scalar. Stem used to name the summary PDF (the file will be <plot.dir>/<filename>.pdf). Default: "af_accuracy_spectra_benchmark".

Value

A named list with three elements:

raw: Data frame of per-draw results with columns n.fluors, draw, method, Mean_Sim, and SD_Sim.
summary: Data frame summarising raw across draws for each (n.fluors, method) combination, with columns n.fluors, method, mean_Mean_Sim, sd_Mean_Sim (variability across draws), and mean_SD_Sim (average within-draw spread).
plot: The ggplot2 object for the summary line plot.

Usage

Arguments

Value

See also