ChemoSpecUtils: plotScores – R documentation

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plotScores

Plot Scores from PCA, MIA or PARAFAC Analysis of a Spectra or Spectra2D Object

Description

Plots the requested scores using the color scheme derived from the Spectra or Spectra2D object. Options are provided to add confidence ellipses for each group in the object. The ellipses may be robust or classical. Option to label the extreme points provided.

Usage

plotScores(
  spectra,
  so,
  pcs = c(1, 2),
  ellipse = "none",
  tol = "none",
  use.sym = FALSE,
  leg.loc = "topright",
  ...
)

Arguments

`spectra`	An object of S3 class `Spectra` or `Spectra2D` object.
`so`	"Score Object" One of the following: An object of class `prcomp`, created by `ChemoSpec` functions `c_pcaSpectra`, `r_pcaSpectra`, `irlba_pcaSpectra` or `s_pcaSpectra`. An object of class `mia` produced by function `miaSpectra2D`. An object of class `parafac` produced by function `pfacSpectra2D`. An object of class `pop` produced by function `popSpectra2D`. Any of the above score objects will have been modified to include a list element called `$method`, a character string describing the pre-processing carried out and the type of PCA performed (used to annotate the plot).
`pcs`	A vector of two integers specifying the components (scores) to plot.
`ellipse`	A character vector specifying the type of ellipses to be plotted. One of `c("both"`, `"none"`, `"cls"`, `"rob")`. `cls` specifies classical confidence ellipses, `rob` specifies robust confidence ellipses. An ellipse is drawn for each group unless there are three or fewer samples in the group.
`tol`	A number describing the fraction of points to be labeled. `tol = 1.0` labels all the points; `tol = 0.05` labels the most extreme 5 percent. Set to `"none"` to completely suppress labels.
`use.sym`	A logical; if TRUE, the color scheme is set to black and the points plotted with symbols. Applies only to `Spectra` objects.
`leg.loc`	Character; if `"none"` no legend will be drawn. Otherwise, any string acceptable to `legend`.
`...`	Additional parameters to be passed to the plotting functions.

Value

None. Side effect is a plot.

Author(s)

Bryan A. Hanson, DePauw University.

Examples

if (checkForPackageWithVersion("ChemoSpec", "5.1")) {
  library("ChemoSpec")
  data(metMUD1)

  pca <- c_pcaSpectra(metMUD1)
  plotScores(metMUD1, pca,
    main = "metMUD1 NMR Data",
    pcs = c(1, 2), ellipse = "cls", tol = 0.05
  )
}

if (checkForPackageWithVersion("ChemoSpec2D", "0.3")) {
  library("ChemoSpec2D")
  data(MUD1)

  res <- miaSpectra2D(MUD1)
  plotScores(MUD1, res, main = "MIA Scores", tol = 0.1, ellipse = "cls")

  set.seed(123)
  res <- pfacSpectra2D(MUD1, parallel = FALSE, nfac = 2)
  plotScores(MUD1, res, tol = 0.1, leg.loc = "bottomright", main = "PARAFAC Score Plot")
}

ChemoSpecUtils

Functions Supporting Packages ChemoSpec and ChemoSpec2D

v0.4.96

GPL-3

Authors

Bryan A. Hanson [aut, cre] (<https://orcid.org/0000-0003-3536-8246>)

Initial release

2021-03-15