A wrapper which carries out sparse PCA analysis on a
`Spectra`

object. The user can select various options for
scaling. There is no normalization by rows - do this manually using
`normSpectra`

. The data will be centered, as is required by PCA.

`s_pcaSpectra(spectra, choice = "noscale", K = 3, para = rep(0.5, K), ...)`

- spectra
An object of S3 class

`Spectra()`

.- choice
A character string indicating the choice of scaling. One of

`c("noscale"`

,`"autoscale"`

,`"Pareto")`

.`"autoscale"`

is called "standard normal variate" or "correlation matrix PCA" in some literature.- K
Integer. The number of components desired.

- para
A vector of

`length(K)`

giving the tuning parameters.- ...
Other parameters to be passed to

`arrayspc`

.

An object of class `prcomp`

and `converted_from_arrayspc`

,
which 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). A check is carried out to see if the computation was successful
and a warning issued if it failed.

The scale choice `autoscale`

scales the columns by their standard
deviation. `Pareto`

scales by the square root of the standard
deviation.

H. Zou, T. Hastie and R. Tibshirani "Sparse Principal Components Analysis"
*J. Comp. Stat. Graphics* vol. 15 no. 2 pgs. 265-286 (2006).

`arrayspc`

for the underlying function,
`c_pcaSpectra`

for classical PCA calculations,
`r_pcaSpectra`

for robust 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()`

.

```
if (FALSE) {
# This example assumes the graphics output is set to ggplot2 (see ?GraphicsOptions).
library("ggplot2")
data(SrE.NMR)
pca <- s_pcaSpectra(SrE.NMR)
p1 <- plotScree(pca)
p1
p2 <- plotScores(SrE.NMR, pca, pcs = c(1, 2), ellipse = "cls", tol = 0.05)
p2 <- p2 + ggtitle("Scores: SrE NMR Data")
p2
p3 <- plotLoadings(SrE.NMR, pca, loads = 1:2, ref = 1)
p3 <- p3 + ggtitle("Loadings: SrE NMR Data")
p3
}
```