R: Interactive 3D Score Plot of a Spectra Object

plotScoresRGL {ChemoSpec} | R Documentation

## Interactive 3D Score Plot of a Spectra Object

### Description

This function uses the `rgl` package to create an interactive plot of PCA scores derived from a `Spectra` object. A title and legend can be added if desired. Classical or robust confidence ellipses may be added if desired.

### Usage

    plotScoresRGL(spectra, pca, pcs = c(1:3), ellipse = TRUE, rob = FALSE,
      cl = 0.95, frac.pts.used = 0.8, title = NULL, t.pos = NULL,
      leg.pos = NULL, lab.opts = FALSE, tol = 0.01, use.sym = FALSE, ...)

### Arguments

`spectra` | An object of S3 class `Spectra`.
`pca` | An object of class `prcomp`.
`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.
`title` | A character string for the plot title.
`t.pos` | A character selection from `LETTERS[1:8]` ( = A through H) indicating the desired location for the title.
`leg.pos` | A character selection from `LETTERS[1:8]` ( = A through H) indicating the desired location for the legend.
`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.
`tol` | Quantile to be used to label extreme data points.
`use.sym` | logical; if true, the color scheme is changed to black and symbols are used for plotting.
`...` | Additional parameters to pass downstream, generally to the plotting routines.

### 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 and legend won't interfere with viewing the data, and use these as arguments for `t.pos` and `leg.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.

### Value

None. Side effect is a plot

### Author(s)

Bryan A. Hanson, DePauw University.

### References

https://github.com/bryanhanson/ChemoSpec

### See Also

Other functions in `ChemoSpec` that plot PCA scores are: `plotScores` (2D version), and `plotScores3D` (uses `lattice` graphics).

### Examples

    ## Not run:

    data(metMUD1)
    pca <- c_pcaSpectra(metMUD1, choice = "autoscale")
    plotScoresRGL(metMUD1, pca, title = "metMUD1 NMR Spectra",
      leg.pos = "A", t.pos = "B")

    ## End(Not run)

[Package ChemoSpec version 4.4.97 Index]