ChemoSpec (version 6.1.10)

r_pcaSpectra: Robust PCA of a Spectra Object

Description

A wrapper which carries out robust PCA analysis on a Spectra object. The data are row- and column-centered, and the user can select various options for scaling.

Usage

r_pcaSpectra(spectra, choice = "noscale")

Value

An object of classes converted_from_princomp and prcomp. It includes a list element called $method, a character string describing the pre-processing carried out and the type of PCA performed (used to annotate plots).

Arguments

spectra

An object of S3 class Spectra().

choice

A character vector describing the type of scaling to be carried out. One of c("noscale", "mad").

Author

Bryan A. Hanson (DePauw University).

References

K. Varmuza and P. Filzmoser Introduction to Multivariate Statistical Analysis in Chemometrics, CRC Press, 2009.

See Also

PCAgrid for the underlying function, c_pcaSpectra for classical PCA calculations, s_pcaSpectra for sparse PCA calculations, irlba_pcaSpectra for PCA via the IRLBA algorithm. Additional documentation at https://bryanhanson.github.io/ChemoSpec/

For displaying the results, ChemoSpecUtils::plotScree(), ChemoSpecUtils::plotScores(), plotLoadings(), plot2Loadings(), sPlotSpectra().

https://bryanhanson.github.io/ChemoSpec/

Examples

if (FALSE) {
# This example assumes the graphics output is set to ggplot2 (see ?GraphicsOptions).
library("ggplot2")
data(metMUD1)
pca <- r_pcaSpectra(metMUD1)

p1 <- plotScree(pca)
p1

p2 <- plotScores(metMUD1, pca, pcs = c(1, 2), ellipse = "cls", tol = 0.05)
p2 <- p2 + ggtitle("Scores: metMUD1 NMR Data")
p2

p3 <- plotLoadings(metMUD1, pca, loads = 1:2, ref = 1)
p3 <- p3 + ggtitle("Loadings: metMUD1 NMR Data")
p3
}