Get Autofluorescence Spectra

Extracts autofluorescence spectra from an unstained samples. Intended for use with unmix.autospectral. Uses FlowSOM (EmbedSOM) clustering for rapid identification of cells with similar AF profiles.

Usage

get.af.spectra(
  unstained.sample,
  asp,
  spectra,
  threads = NULL,
  som.dim = 10,
  figures = TRUE,
  plot.dir = NULL,
  table.dir = NULL,
  title = NULL,
  verbose = TRUE
)

Arguments

unstained.sample

Path and file name for a unstained sample FCS file. The sample type and processing (protocol) method should match the fully stained samples to which the AF will be applied, ideally.

asp

The AutoSpectral parameter list.

spectra

Spectral signatures of fluorophores, normalized between 0 and 1, with fluorophores in rows and detectors in columns.

threads

Numeric. Number of threads to use for parallel processing in the creation of the SOM. Default NULL reverts to asp$worker.process.n.

som.dim

Number of x and y dimensions for the SOM. Default is 10.

figures

Logical, whether to plot the spectral traces and heatmap for the AF signatures. Default is TRUE.

plot.dir

Directory (folder) where the plots will be saved. Default is NULL, which inherits from asp$figure.af.dir.

table.dir

Directory (folder) where the spectra csv file will be saved. Default is NULL, which inherits from asp$table.af.dir.

title

Title for the output spectral plots and csv file. Default is Autofluorescence spectra.

verbose

Logical, controls messaging. Default is TRUE.

Value

A matrix of autofluorescence spectra.