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

### See Also

`Mclust` for background on the method.

### 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]