Get Fluorophore Spectra

This function retrieves the fluorophore spectra for flow cytometry data, optionally using cleaned expression data. It also plots and saves the spectra, and performs cosine similarity QC for controls.

Usage

get.fluorophore.spectra(
  flow.control,
  asp,
  use.clean.expr = TRUE,
  af.spectra = NULL,
  title = NULL,
  figures = TRUE,
  refine = FALSE,
  control.dir = NULL,
  control.def.file = NULL,
  refine.args = list()
)

Arguments

flow.control

A list containing flow cytometry control data.

asp

The AutoSpectral parameter list. Prepare using get.autospectral.param

use.clean.expr

Logical indicating whether to use cleaned expression data, default is TRUE

af.spectra

Optional autofluorescence spectra to include.

title

Optional prefix for plot titles, default is NULL, which gives "Initial" when use.clean.expr is FALSE and "Clean" when use.clean.expr is TRUE.

figures

Logical, default is TRUE. Whether to produce plots of the fluorophore spectra and cosine similarity.

refine

Logical, default FALSE. Whether to re-measure each row directly on its own single-color control after the first pass, via refine.fluorophore.spectra(). Unlike the first pass, this re-reads the controls fresh from control.dir/control.def.file, one file at a time, rather than using flow.control's already-gated and possibly downsampled data – checking a spectrum against the same selection it was fit from cannot surface bias that selection introduced. Requires control.dir and control.def.file.

control.dir, control.def.file

As in define.flow.control(). Ignored unless refine = TRUE, in which case both are required and should normally be the same files flow.control was built from.

refine.args

Named list of further arguments passed to refine.fluorophore.spectra() when refine = TRUE.

Value

A matrix with the fluorophore spectra. When refine = TRUE, also carries attr(., "refine.log") and attr(., "refine.crosstalk") with the per-iteration diagnostics.