R: Plot PCA Loadings for a Spectra Object

plotLoadings {ChemoSpec} | R Documentation

## Plot PCA Loadings for a Spectra Object

### Description

Creates a multi-panel plot of loadings along with a reference spectrum.

### Usage

    plotLoadings(spectra, pca, loads = c(1), ref = 1, ...)

### Arguments

`spectra` | An object of S3 class `Spectra`.
`pca` | An object of class `prcomp`, modified to include a list element called `$method`, a character string describing the pre-processing carried out and the type of PCA performed (it appears on the plot). This is automatically provided if `ChemoSpec` functions `c_pcaSpectra` or `r_pcaSpectra` were used to create `pca`.
`loads` | An integer vector giving the loadings to plot. More than 3 loadings creates a useless plot using the default graphics window.
`ref` | An integer specifying the reference spectrum to plot, which appears at the bottom of the plot.
`...` | Additional parameters to be passed to plotting functions.

### Value

None. Side effect is a plot.

### Author(s)

Bryan A. Hanson, DePauw University.

### References

https://github.com/bryanhanson/ChemoSpec

### See Also

See `plot2Loadings` to plot two loadings against each other, and `sPlotSpectra` for an alternative approach.

### Examples

    data(SrE.IR)
    pca <- c_pcaSpectra(SrE.IR, choice = "noscale")
    myt <- expression(bolditalic(Serenoa)~bolditalic(repens)~bold(IR~Spectra))
    plotLoadings(SrE.IR, pca, main = myt,
    	 loads = 1:2, ref = 1)

[Package ChemoSpec version 4.4.97 Index]