Spectral Reference Plot — spectral.reference.plot • AutoSpectral

This function plots a comparison between the user's fluorophore spectrum, from spectra, and a known reference spectrum (if available) for the same fluorophore. Quality control is performed using cosine similarity between the two spectral profiles.

Usage

spectral.reference.plot(
  spectra,
  asp,
  fluorophore = rownames(spectra),
  qc.threshold.warn = 0.98,
  qc.threshold.fail = 0.9,
  experiment.control.color = "black",
  library.reference.color = "blue",
  comparison.color = "red",
  experiment.line.type = "solid",
  library.line.type = "dotted",
  comparison.line.type = "dashed",
  pass.color = "darkgreen",
  warn.color = "darkorange",
  fail.color = "red",
  linewidth = 1,
  plot.dir = "./figure_spectra",
  filename = "spectral_qc_report.pdf",
  comparison.spectra = NULL,
  comparison.label = "Pre-refinement",
  highlight.fluors = character(0L)
)

Arguments

spectra: Matrix or dataframe containing spectral data. This should be in format fluorophores x detectors. Row names are used to label each trace (e.g. sample identifiers, which may disambiguate multiple controls for the same fluorophore) and column names will be used as the detectors (channels).
asp: The AutoSpectral parameter list. Used to determine which cytometer produced the data.
fluorophore: Optional character vector, the same length and order as nrow(spectra), giving the true fluorophore identity of each row. Used to look up the library reference spectrum and any comparison.spectra. Defaults to rownames(spectra), matching the previous behavior when each row already corresponds to a single, uniquely-named fluorophore.
qc.threshold.warn: Numeric, default 0.98. The similarity value to trigger a QC warning.
qc.threshold.fail: Numeric, default 0.90. The similarity value to trigger a QC failure.
experiment.control.color: Color for the line representing the user's fluorophore spectrum from the single-stained reference control. Default is black.
library.reference.color: Color for the line representing the library reference standard fluorophore spectrum. Default is "blue".
comparison.color: Color for the optional comparison spectrum. Default is "red".
experiment.line.type: Line style for the line representing the user's fluorophore spectrum from the single-stained reference control. Default is "solid".
library.line.type: Line style for the line representing the library reference standard fluorophore spectrum. Default is "dotted".
comparison.line.type: Line style for the line representing the optional comparison spectrum. Default is "dashed".
pass.color: Color to label similarity values above the qc.threshold.warn, i.e., fluorophores passing QC. Default is darkgreen.
warn.color: Color to label similarity values above the qc.threshold.fail but below the qc.threshold.warn, i.e., fluorophores in a potentially problematic zone. Default is darkorange.
fail.color: Color to label similarity values below the qc.threshold.fail, i.e., fluorophores failing QC. Default is red.
linewidth: Width of the line for the spectral traces. Default is 1.
plot.dir: Directory where the files will be saved. Default is ./figure_spectra.
filename: Name for the output PDF file. Default is spectral_qc_report.pdf.
comparison.spectra: Optional matrix of additional spectral profiles to be plotted as comparisons. Used for get.spectra.automated for legacy fallback.
comparison.label: Optional character string, default "Pre-refinement", for the comparison.spectra.
highlight.fluors: Optional numeric for differentiating comparison fluors in the plots with the "refined" tag.

Value

None. Plots are saved to a PDF in plot.dir.