feemflame: Fluorescence and scAttering Model Estimation

In albatross: PARAFAC Analysis of Fluorescence Excitation-Emission Matrices

Fluorescence and scAttering Model Estimation

Description

Given a FEEM cube, model the fluorescence and the scattering signals at the same time as a sum of a PARAFAC model and a low-rank unfolded matrix factorisation.

Usage

  feemflame(
    X, ffac, sfac, maxiter = 32, widths = rep(25, 4), Raman.shift = 3400,
    ctol = 1e-04, progress = TRUE, control.parafac, control.cmf
  )
  ## S3 method for class 'feemflame'
fitted(object, ...)
  ## S3 method for class 'feemflame'
residuals(object, ...)
  ## S3 method for class 'feemflame'
coef(
    object, type = c(
      "fluorescence",
      "scores", "loadings", "emission", "excitation", "samples",
      "scattering", "sc.scores", "sc.loadings"
    ), ...
  )
  ## S3 method for class 'feemflame'
plot(
    x, type = c('both', 'fl.image', 'fl.lines'), ...
  )

Arguments

X	A feemcube object.
ffac	The number of trilinear components used to model fluorescence, passed to feemparafac.
sfac	The number of bilinear (low-rank matrix factorisation) components used to model the scattering signal.
maxiter	Maximum number of alternating PARAFAC and constrained matrix factorisation iterations.
widths	Widths of the scattering regions, like in feemscatter: A numeric vector of length 4 containing the widths (in nm) of the scattering signal, in the following order: Rayleigh scattering Raman scattering Rayleigh scattering, 3{2\lambda 2 lambda2λ \item Raman scattering, 3{2\lambda

2 lambda2λ

Details

FLAME models the input data as a sum of fluorescence signal (PARAFAC model) and scattering signal (low rank model):

3{ X_k(\lambda^\mathrm{em}_i, \lambda^\mathrm{ex}_j) = \underbrace{\sum_p A_{i,p} B_{j,p} C_{k,p}}_{\mbox{fluorescence}} + \underbrace{\sum_q S_{i,j,q} D_{k,q}}_{\mbox{scattering}}

Value

feemflame	An object of class feemflame, which is a list containing the following components: fl A feemparafac object containing the fluorescence part of the model. sc An object of internal class cmf. Please don't rely on its structure.
fitted.feemflame	A feemcube object containing the part of X fitted by the model.
residuals.feemparafac	A feemcube object equal to 3{ \mathbf{X} - \hat{\mathbf{X}}

X - fitted(X)<b>X</b> - <b>X&#x0302;</b>, with an extra class feem.resid set. Objects of this class are plotted with a different default palette, see plot.feem.resid.

Note

The structure of the feemflame object, the initialisation, and the constraints may be subject to change in a future version.

References

\reference

Tauler1998

\reference

Krylov2021 https://files.libs.chem.msu.ru/~ivan/SSC17/P13.pdf.

See Also

feemparafac, feemcube

Examples

  data(feems)
  cube <- feemscale(cube)
  factors <- feemflame(cube, ffac = 3, sfac = 1)
  str(coef(factors))
  str(coef(factors, 'scattering'))
  plot(factors)

albatross documentation built on May 29, 2024, 9:10 a.m.