R: 3D PCA Score Plot for a Spectra Object

plotScores3D {ChemoSpec} | R Documentation

## 3D PCA Score Plot for a Spectra Object

### Description

Creates a basic 3D plot of PCA scores from the analysis of a `Spectra` object, color coded according the to scheme stored in the object.

### Usage

    plotScores3D(spectra, pca, pcs = c(1:3), ellipse = TRUE, rob = FALSE,
      cl = 0.95, frac.pts.used = 0.8, view = list(y = 34, x = 10, z = 0),
      tol = 0.01, use.sym = FALSE, ...)

### Arguments

`spectra` | An object of S3 class `Spectra`.
`pca` | An object of class `prcomp`, modified to include a list element called `$method`, a character string describing the pre-processing carried out and the type of PCA performed (it appears on the plot). This is automatically provided if `ChemoSpec` functions `c_pcaSpectra` or `r_pcaSpectra` were used to create `pca`.
`pcs` | A vector of three integers specifying the PCA scores to plot.
`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.
`view` | A list of viewing transformations to be applied to the data. May contain values for x, y and z axes; keep in mind that the order of the transformations is important. For example, specifying `view = list(x = 45, y = 10)` produces a different view than `view = list(y = 10, x = 45)`. The list may be as along as you like - the series of transformations representing an accumulation of tweaks to achieve the desired view.
`tol` | Quantile to be used to label extreme data points. Currently not used - need to fix the code!
`use.sym` | logical; if true, the color scheme is change to black and symbols are used for plotting.
`...` | Other parameters to be passed downstream.

### Value

None. Side effect is a plot.

### Author(s)

Bryan A. Hanson, DePauw University.

### References

https://github.com/bryanhanson/ChemoSpec

### See Also

For a 2D plot of the scores, see `plotScores`. For interactive 3D plots, use `plotScoresRGL`.

### Examples

    data(metMUD1)
    pca <- c_pcaSpectra(metMUD1, choice = "noscale")
    plotScores3D(metMUD1, pca, main = "metMUD1 NMR Spectra")

[Package ChemoSpec version 4.4.97 Index]