plotHCA

An object of S3 class <code><a href="/link/Spectra?package=ChemoSpec&version=4.1.15" rd-options="" data-mini-rdoc="ChemoSpec::Spectra">Spectra</a></code>.

spectra

A <code><a href="/link/hclust?package=ChemoSpec&version=4.1.15" rd-options="" data-mini-rdoc="ChemoSpec::hclust">hclust</a></code> object.

hclst

sub.title

Logical; if true, the color scheme will be black and lower-case letters will be used to indicate group membership.

use.sym

Character; if <code>"none"</code> no legend will be drawn.  Otherwise, any string acceptable to <code><a href="/link/legend?package=ChemoSpec&version=4.1.15" rd-options="" data-mini-rdoc="ChemoSpec::legend">legend</a></code>.

leg.loc

Additional parameters to be passed to the plotting routines.

This function plots the results of an HCA analysis of a <code><a href="/link/Spectra?package=ChemoSpec&version=4.1.15" rd-options="" data-mini-rdoc="ChemoSpec::Spectra">Spectra</a></code> object.  This is not called directly by the user -- <code><a href="/link/hcaSpectra?package=ChemoSpec&version=4.1.15" rd-options="" data-mini-rdoc="ChemoSpec::hcaSpectra">hcaSpectra</a></code> and <code><a href="/link/hcaScores?package=ChemoSpec&version=4.1.15" rd-options="" data-mini-rdoc="ChemoSpec::hcaScores">hcaScores</a></code> use it (see those pages for examples).

multivariate

hplot

cluster

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.

plotHCA: Plot Dendrogram for Spectra Object

Description

Usage

Arguments

Value

References