R: Plot ANOVA-PCA Scores from a Spectra Object

aovPCAscores {ChemoSpec} | R Documentation

## Plot ANOVA-PCA Scores from a Spectra Object

### Description

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

### 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`. For example, you can plot confidence ellipses this way. Note that ellipses are drawn based on the groups in `spectra$groups`, but the separation done by `aov_pcaSpectra` is based on argument `fac`. These may not correspond, but you can edit `spectra$groups` to match if necessary.

### Value

Returns the PCA results, and creates the requested plot.

### Author(s)

Matthew J. Keinsley and Bryan A. Hanson, DePauw University.

### 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`.

[Package ChemoSpec version 4.4.97 Index]