R: Plot PCA Scores of a Spectra Object

plotScores {ChemoSpec}

R Documentation

Plot PCA Scores of a Spectra Object

Description

Plots the requested PCA scores using the color scheme derived from a Spectra object. Options are provided to add confidence ellipses for each group in the object. The ellipses may be robust or classical. Option to label the extreme points provided.

Usage

plotScores(spectra, pca, pcs = c(1, 2), ellipse = "none", tol = "none",
  use.sym = FALSE, leg.loc = "topright", ...)

Arguments

`spectra`	An object of S3 class `Spectra`.
`pca`	An object of class `prcomp`, modified to include a list element called `$method`, a character string describing the pre-processing carried out and the type of PCA performed (it appears on the plot). This is automatically provided if `ChemoSpec` functions `c_pcaSpectra` or `r_pcaSpectra` were used to create `pca`.
`pcs`	A vector of two integers specifying the PCA scores to plot.
`ellipse`	A character vector specifying the type of ellipses to be plotted. One of `c("both", "none", "cls", "rob")`. `cls` specifies classical confidence ellipses, `rob` specifies robust confidence ellipses. An ellipse is drawn for each group in `spectra$groups`.
`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.
`use.sym`	A logical; if true, the color scheme is set to black and the points plotted with symbols.
`leg.loc`	Character; if `"none"` no legend will be drawn. Otherwise, any string acceptable to `legend`.
`...`	Additional parameters to be passed to the plotting functions.

Value

None. Side effect is a plot.

Author(s)

Bryan A. Hanson, DePauw University.

References

https://github.com/bryanhanson/ChemoSpec

Examples


data(metMUD1)
pca <- c_pcaSpectra(metMUD1)
plotScores(metMUD1, pca, main = "metMUD1 NMR Data",
	 pcs = c(1,2), ellipse = "cls", tol = 0.05)

[Package ChemoSpec version 4.4.97 Index]