r_pcaSpectra: Robust PCA of a Spectra Object

Description Usage Arguments Value Author(s) References See Also Examples

View source: R/r_pcaSpectra.R

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

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r_pcaSpectra(spectra, choice = "noscale")

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").

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).

Author(s)

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/

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

Examples

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## Not run: 
# 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

## End(Not run)

bryanhanson/ChemoSpec documentation built on Jan. 9, 2022, 6:41 p.m.