ChemoSpec (version 6.1.10)

plot3dScores: 3D PCA Score Plot for a Spectra Object

Description

Creates an interactive 3D plot of PCA scores from the analysis of a Spectra object, color coded according the to scheme stored in the object. The plot is created by plotly and appears in a browser window.

Usage

plot3dScores(
  spectra,
  pca,
  pcs = c(1:3),
  ellipse = TRUE,
  rob = FALSE,
  cl = 0.95,
  frac.pts.used = 0.8
)

Value

None. Side effect is a plot in a browser window.

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.

Author

Bryan A. Hanson (DePauw University).

See Also

Additional documentation at https://bryanhanson.github.io/ChemoSpec/

Examples

if (interactive()) {
  data(metMUD1)
  pca <- c_pcaSpectra(metMUD1, choice = "noscale")
  p <- plot3dScores(metMUD1, pca)
  p
}