ChemoSpecUtils (version 1.0.5)

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",
  ...
)

Value

The returned value depends on the graphics option selected (see GraphicsOptions()).

• base: None. Side effect is a plot.

• ggplot2: The plot is displayed, and a ggplot2 object is returned if the value is assigned. The plot can be modified in the usual ggplot2 manner.

Arguments

spectra

An object of S3 class ChemoSpec::Spectra() or ChemoSpec2D::Spectra2D().

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 approximately the most extreme 5 percent. Set to 'none' to completely suppress labels. Note that a simple approach based upon quantiles is used, assumes that both x and y are each normally distributed, and treats x and y separately. Thus, this is not a formal treatment of outliers, just a means of labeling points. Groups are lumped together for the computation.

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

Either a list with elements x and y, or a string like 'topright'. Values in a list should be on [0,1], i.e. the lower left of the plot area is 0,0 and the upper right is 1,1. Allowed string values are those described in graphics::legend() under 'Details'. A value of 'none' is acceptable as well.

...

Parameters to be passed to the plotting routines. Applies to base graphics only.

Author

Bryan A. Hanson (DePauw University), Tejasvi Gupta.

Examples

if (checkForPackageWithVersion("ChemoSpec", 6.0)) {
  library("ChemoSpec")
  # This example assumes the graphics output is set to ggplot2 (see ?GraphicsOptions).
  library("ggplot2")
  data(metMUD1)

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

if (checkForPackageWithVersion("ChemoSpec2D", 0.5)) {
  library("ChemoSpec2D")
  library("ggplot2")
  data(MUD1)

  mia <- miaSpectra2D(MUD1)
  p1 <- plotScores(MUD1, mia, tol = 0.1, ellipse = "cls")
  p1 <- p1 + ggtitle("MIA Scores")
  p1

  set.seed(123)
  pfac <- pfacSpectra2D(MUD1, parallel = FALSE, nfac = 2)
  p2 <- plotScores(MUD1, pfac, tol = 0.1, leg.loc = "bottomright")
  p2 <- p2 + ggtitle("PARAFAC Score Plot")
  p2
}