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

### See Also

For other ways of displaying the results, `plotScree`, `plotLoadings`, `plot2Loadings`. For a 3D plot of the scores, see `plotScores3D`, or `plotScoresRGL` for an interactive version.

### 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]