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)

For a 2D plot of the scores, see `plotScores`. For interactive 3D plots, use `plotScoresRGL`. Additional documentation at https://bryanhanson.github.io/ChemoSpec/
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