labelExtremes3d


A matrix of 3 columns containing x, y and z values for the labels, with rows corresponding to sample names.


data


A character vector of sample names; must have length equal to <code>nrow(data)</code>.


names


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 <em>approximately</em> the most extreme 5 percent.  Note that this is simply based upon quantiles, assumes that x, y and z are each normally distributed, and treats x, y and yz separately.  Thus, this is not a formal treatment of outliers, just a means of labeling points.  Note too that while this function could deal with groups separately, the way it is called by <code><a rd-options="" href="/link/plotScoresRGL?package=ChemoSpec&version=4.3.34" data-mini-rdoc="ChemoSpec::plotScoresRGL">plotScoresRGL</a></code> lumps all groups together.



A utility function to identify the extreme values in a 3D plot data set, presumably so that they can be labeled.  Algorithm is similar to <code><a rd-options="" href="/link/labelExtremes?package=ChemoSpec&version=4.3.34" data-mini-rdoc="ChemoSpec::labelExtremes">labelExtremes</a></code>, except that <code>labelExtremes3d</code> does not do the plotting (because the results are used by functions that use different plotting paradigms).  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

labelExtremes3d function


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 <em>approximately</em> the most extreme 5 percent.  Note that this is simply based upon quantiles, assumes that x, y and z are each normally distributed, and treats x, y and yz separately.  Thus, this is not a formal treatment of outliers, just a means of labeling points.  Note too that while this function could deal with groups separately, the way it is called by <code><a rd-options='' href='plotScoresRGL'>plotScoresRGL</a></code> lumps all groups together.



A utility function to identify the extreme values in a 3D plot data set, presumably so that they can be labeled.  Algorithm is similar to <code><a rd-options='' href='labelExtremes'>labelExtremes</a></code>, except that <code>labelExtremes3d</code> does not do the plotting (because the results are used by functions that use different plotting paradigms).  An internal function, not generally called by the user.


labelExtremes3d: Identify Extreme Values in 3D

Description

Usage

Arguments

Value

References