Spectral Reference Plot

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,
  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 will be used as the fluorophore names. Column names will be used as the detectors (channels).

asp

The AutoSpectral parameter list. Used to determine which cytometer produced the data.

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.