plotScoresDecoration

An object of S3 class <code><a rd-options="" href="/link/Spectra?package=ChemoSpec&version=4.4.97" data-mini-rdoc="ChemoSpec::Spectra">Spectra</a></code>.

spectra

An object of class <code><a rd-options="" href="/link/prcomp?package=ChemoSpec&version=4.4.97" 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). This is automatically provided if <code>ChemoSpec</code> functions
<code><a rd-options="" href="/link/c_pcaSpectra?package=ChemoSpec&version=4.4.97" data-mini-rdoc="ChemoSpec::c_pcaSpectra">c_pcaSpectra</a></code> or <code><a rd-options="" href="/link/r_pcaSpectra?package=ChemoSpec&version=4.4.97" data-mini-rdoc="ChemoSpec::r_pcaSpectra">r_pcaSpectra</a></code> were used to create
<code>pca</code>.

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 rd-options="" href="/link/Spectra?package=ChemoSpec&version=4.4.97" 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) and model-based clustering. 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.

Bryan Hanson

ChemoSpec

Exploratory Chemometrics for Spectroscopy

Bryan A. Hanson

Mike Bostock

plotScoresDecoration function

An object of S3 class <code><a rd-options='' href='Spectra'>Spectra</a></code>.

An object of class <code><a rd-options='' href='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). This is automatically provided if <code>ChemoSpec</code> functions
<code><a rd-options='' href='c_pcaSpectra'>c_pcaSpectra</a></code> or <code><a rd-options='' href='r_pcaSpectra'>r_pcaSpectra</a></code> were used to create
<code>pca</code>.

Utility function to carry out misc. labeling functions on the PCA score plot
of a <code><a rd-options='' href='Spectra'>Spectra</a></code> object. An internal function, not generally
called by the user.

plotScoresDecoration: Decorate PCA Score Plot of a Spectra Object

Description

Usage

Arguments

Value

References