R: mclust Analysis of a Spectra Object PCA Results

mclustSpectra {ChemoSpec}

R Documentation

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.

Author(s)

Bryan A. Hanson, DePauw University.

References

https://github.com/bryanhanson/ChemoSpec

Examples


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)

[Package ChemoSpec version 4.4.97 Index]