ChemoSpec (version 5.0.88)

mclustSpectra: mclust Analysis of a Spectra Object PCA Results

Description

This function is a wrapper for the Mclust function and associated plotting functions.

Usage

mclustSpectra(spectra, pca, pcs = c(1:3), dims = c(1, 2),
  plot = c("BIC", "proj", "error"), use.sym = FALSE, ...)

Arguments

spectra

An object of S3 class Spectra.

pca

An object of class prcomp.

pcs

An integer vector describing which PCs to use.

dims

A integer vector giving the PCA dimensions to use.

plot

A character string indicating what plot to make. Options are c("BIC", "proj", "error"); see Mclust for details.

use.sym

Logical; if true, the color scheme is changed to black and symbols are used for plotting.

…

Other parameters to be passed downstream.

Value

The Mclust model is returned invisibly, and a plot is made.

References

https://github.com/bryanhanson/ChemoSpec

See Also

Mclust for background on the method.

Examples

# NOT RUN {
require("mclust")
data(SrE.IR)
class <- c_pcaSpectra(SrE.IR, choice = "autoscale")
mclustSpectra(SrE.IR, class, main = "Cuticle IR", plot = "BIC")
mclustSpectra(SrE.IR, class, main = "Cuticle IR", plot = "proj")
mclustSpectra(SrE.IR, class, main = "Cuticle IR", plot = "error",
	 truth = metMUD1$groups)

# }