plotScoresDecoration

An object of S3 class <code><a href="/link/Spectra?package=ChemoSpec&version=4.0.6" rd-options="" data-mini-rdoc="ChemoSpec::Spectra">Spectra</a></code>.

spectra

An object of class <code><a href="/link/prcomp?package=ChemoSpec&version=4.0.6" rd-options="" data-mini-rdoc="ChemoSpec::prcomp">prcomp</a></code>, modified to include a list element called <code>$method</code>, a character string describing the pre-processing carried out and the type of PCA performed (it appears on the plot).

A vector of two integers specifying the PCA scores to plot.

A number describing the fraction of points to be labeled.  <code>tol = 1.0</code> labels all the points; <code>tol = 0.05</code> labels the most extreme 5 percent.

Utility function to carry out misc. labeling functions on the PCA score plot of a <code><a href="/link/Spectra?package=ChemoSpec&version=4.0.6" rd-options="" data-mini-rdoc="ChemoSpec::Spectra">Spectra</a></code> object.  An internal function, not generally called by the user.

utilities

A collection of functions for top-down exploratory data analysis of spectral data obtained via nuclear magnetic resonance (NMR), infrared (IR) or Raman spectroscopy.  Includes functions for plotting and inspecting spectra, peak alignment, hierarchical cluster analysis (HCA), principal components analysis (PCA), model-based clustering and statistical total correlation spectroscopy (STOCSY) analysis.  Robust methods appropriate for this type of high-dimensional data are available.  ChemoSpec is designed with metabolomics data sets in mind, where the samples fall into groups such as treatment and control.  Graphical output is formatted consistently for publication quality plots.  ChemoSpec is intended to be very user friendly and help you get usable results quickly.  A vignette covering typical operations is available.

plotScoresDecoration: Decorate PCA Score Plot of a Spectra Object

Description

Usage

Arguments

Value

References