R: Plot PCA Loadings from a Spectra Object Against Each Other

plot2Loadings {ChemoSpec} | R Documentation

## Plot PCA Loadings from a Spectra Object Against Each Other

### Description

Plots two PCA loadings specified by the user, and labels selected (extreme) points. Typically used to determine which variables (frequencies) are co-varying, although in spectroscopy most peaks are represented by several variables and hence there is a lot of co-varying going on. Also useful to determine which variables are contributing the most to the clustering on a score plot.

### Usage

    plot2Loadings(spectra, pca, loads = c(1, 2), tol = 0.05, ...)

### 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` | A vector of two integers specifying which loading vectors to plot.
`tol` | A number describing the fraction of points to be labeled. `tol = 1.0` labels all the points; `tol = 0.05` labels the most extreme 5 percent.
`...` | Other parameters to be passed to the plotting routines.

### Value

None. Side effect is a plot.

### Author(s)

Bryan A. Hanson, DePauw University.

### References

https://github.com/bryanhanson/ChemoSpec

### See Also

See `plotLoadings` to plot one loading against the original variable (frequency) axis. See `sPlotSpectra` for a different approach.

### Examples

    data(SrE.IR)
    pca <- c_pcaSpectra(SrE.IR)
    myt <- expression(bolditalic(Serenoa)~bolditalic(repens)~bold(IR~Spectra))
    res <- plot2Loadings(SrE.IR, pca, main = myt,
    	 loads = c(1,2), tol = 0.001)

[Package ChemoSpec version 4.4.97 Index]