mclust Analysis of a Spectra Object PCA Results

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

mclustSpectra(
  spectra,
  pca,
  pcs = c(1:3),
  dims = c(1, 2),
  plot = c("BIC", "proj", "errors"),
  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.

See also

Mclust for background on the method. Additional documentation at https://bryanhanson.github.io/ChemoSpec/

Author

Bryan A. Hanson (DePauw University).

Examples

if (FALSE) {
require("mclust")
data(metMUD1)
cls <- c_pcaSpectra(metMUD1, choice = "autoscale")

p <- plotScores(metMUD1, cls)

mclustSpectra(metMUD1, cls, plot = "BIC")
mclustSpectra(metMUD1, cls, plot = "proj")
mclustSpectra(metMUD1, cls, plot = "errors", truth = metMUD1$groups)
}