Read In Saved Spectra

Reads in CSV files created by AutoSpectral or in the same format (fluorophores in rows, detectors in columns, first row is detector names, first column contains fluorophore names).

Usage

read.spectra(
  spectra.file,
  spectra.dir = "./table_spectra",
  remove.af = FALSE,
  af.param = "AF",
  check.collinearity = TRUE,
  collinearity.threshold = 0.95
)

Arguments

spectra.file

File name for the spectra CSV file to be read.

spectra.dir

File path to the folder containing spectra.file. Default is table_spectra, where AutoSpectral saves the spectra files.

remove.af

Logical, default is FALSE. If TRUE, returns the spectral matrix without the default autofluorescence spectrum.

af.param

Name of the autofluorescence parameter. Default is AF. Note that any fluorophores can be removed from the matrix by supplying a character vector, e.g., c("BUV395", "PE"), if desired.

check.collinearity

Logical, default TRUE. CSV files cannot carry the "fluorophore" identity attribute that check.spectra.duplicates() checks exactly elsewhere, and a sample-disambiguated rowname (e.g. "PE (cells)" / "PE (cells) (CD4)") is unique by construction, so a rownames-only check would never catch two controls for the same dye. When TRUE, screens for suspiciously similar rows as an early, load-time warning (the same screen check.spectra.duplicates() falls back to later).

collinearity.threshold

Numeric, default 0.95. Cosine similarity above which two rows trigger the warning. Matches the package default for asp$similarity.warning.n.

Value

A matrix containing the fluorophore spectra (fluorophore x detectors).