plot2Loadings: 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.

References

https://github.com/bryanhanson/ChemoSpec

Examples

Run this code

# NOT RUN {
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)

# }