R: mclust Analysis of a Spectra Object in 3D

mclust3dSpectra {ChemoSpec} | R Documentation

## mclust Analysis of a Spectra Object in 3D

### Description

This function conducts an mclust analysis of the PCA results of a `Spectra` object and displays the results in 3D. Classical or robust confidence ellipses can be added if desired. Improperly classified data points can be marked. rgl graphics are employed.

### Usage

    mclust3dSpectra(spectra, pca, pcs = c(1:3), ellipse = TRUE, rob = FALSE,
      cl = 0.95, frac.pts.used = 0.8, truth = NULL,
      title = "no title provided", t.pos = NULL, lab.opts = FALSE,
      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.
`ellipse` | Logical indicating if confidence ellipses should be drawn.
`rob` | Logical; if `ellipse = TRUE`, indicates that robust confidence ellipses should be drawn. If `FALSE`, classical confidence ellipses are drawn.
`cl` | A number indicating the confidence interval for the ellipse.
`frac.pts.used` | If `ellipse = TRUE` and `rob = TRUE`, a number indicating the fraction of the data points to be considered "good" and thus used to compute the robust confidence ellipse.
`truth` | A character vector indicating the known group membership for reach row of the PC scores. Generally this would be `spectra$groups`. #' @param title A character string for the plot title.
`title` | A character string giving the title.
`t.pos` | A character selection from `LETTERS[1:8]` ( = A through H) indicating the desired location for the title.
`lab.opts` | A logical indicating whether or not to display the locations where the title and legend can be placed. These locations are the corners of a cube surrounding the data.
`use.sym` | Logical; if true, the color scheme is changed to black and symbols are used for plotting.
`...` | Other parameters to be passed downstream.

### Details

If you intend to make a hard copy of your plot, use `lab.opts = TRUE` until you have found a good view of your data. Then note corners of the cube where the title won't interfere with viewing the data, and use this for `t.pos`, and add `title`. Adjust as necessary, then turn off label display using `lab.opts = FALSE`. Back at the console, use `> rgl.snapshot("file_name.png")` to create the hardcopy.

Note that the confidence ellipses computed here are generated independently of the `Mclust` results - they do not correspond to the ellipses seen in 2D plots from `Mclust`.

### Value

The mclust model is returned invisibly, and a plot is produced.

### Author(s)

Bryan A. Hanson, DePauw University.

### References

https://github.com/bryanhanson/ChemoSpec

### See Also

`Mclust` for background on the method.

### Examples

    ## Not run:

    require(mclust)
    data(metMUD1)
    class <- c_pcaSpectra(metMUD1)
    mclust3dSpectra(metMUD1, class, title = "mclust3dSpectra demo",
    	 lab.opts = FALSE, t.pos = "A")

    ## End(Not run)

[Package ChemoSpec version 4.4.97 Index]