ChemoSpec (version 4.3.34)

aovPCAscores: Plot ANOVA-PCA Scores from a Spectra Object

Description

Uses the results from aov_pcaSpectra to conduct PCA and plot the scores.

Usage

aovPCAscores(spectra, LM, plot = 1, type = "class", choice = NULL, ...)

Arguments

spectra

An object of S3 class Spectra.

LM

List of matrices created by aov_pcaSpectra.

plot

An integer specifying which scores to plot.

type

Either classical ("cls") or robust ("rob"); Results in either c_pcaSpectra or r_pcaSpectra being called on the Spectra object.

choice

The type of scaling to be performed. See c_pcaSpectra and r_pcaSpectra for details.

...

Additional parameters to be passed to plotScores.

Value

Returns the PCA results, and creates the requested plot.

Details

Argument plot is used to select a matrix from those in LM. The residual error matrix is then added to the selected matrix before performing PCA. Use names(LM) to see which factor is stored in which matrix.

References

Pinto, Bosc, Nocairi, Barros, and Rutledge. "Using ANOVA-PCA for Discriminant Analysis: ..." Analytica Chimica Acta 629.1-2 (2008): 47-55.

Harrington, Vieira, Espinoza, Nien, Romero, and Yergey. "Analysis of Variance--Principal Component Analysis: ..." Analytica Chimica Acta 544.1-2 (2005): 118-27.

https://github.com/bryanhanson/ChemoSpec

See Also

The use of this function can be seen in aov_pcaSpectra. See also plotScores.