Build A Continuous Autofluorescence Basis From The Discrete Library

Constructs a low-dimensional basis for autofluorescence that replaces the discrete AF library in the unmixing solve. The basis is derived from the part of the AF library that the fluorophore panel cannot explain, because only that component is identifiable and only that component reaches the fluorophore abundances. Ranking by out-of-span energy rather than total energy means the leading directions are the ones that actually matter, and it makes the resulting normal equations diagonal, so the per-cell solve is a single projection with no matrix inverse.

Usage

get.af.basis.library(
  af.spectra,
  spectra,
  n.components = NULL,
  var.explained = 0.99
)

Arguments

af.spectra

Autofluorescence spectra, variants in rows and detectors in columns. Prepare using get.af.spectra.

spectra

Fluorophore spectral signatures, fluorophores in rows and detectors in columns.

n.components

Integer, number of basis directions to retain. Default NULL, in which case the count is chosen from var.explained.

var.explained

Numeric in (0, 1], default 0.99. Fraction of the out-of-span variance of the AF library the retained basis must capture. Ignored when n.components is supplied.

Value

A list with basis (detectors x components), sigma (singular values of the projected library), directions (the orthonormal out-of-span directions, detectors x components), var.explained (cumulative fraction captured) and n.components.