ChemoSpec: plotScores3D – R documentation

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plotScores3D

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.

Examples

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

ChemoSpec

Exploratory Chemometrics for Spectroscopy

v5.3.11

GPL-3

Authors

Bryan A. Hanson [aut, cre] (<https://orcid.org/0000-0003-3536-8246>), Mike Bostock [cph, ctb] (author of the d3.js library used by plotSpectraJS, http://d3js.org), Matt Keinsley [ctb] (author of initial AOV-PCA code)

Initial release

2021-03-24