A collection of functions for exploratory chemometrics of 2D spectroscopic data sets such as COSY (correlated spectroscopy) and HSQC (heteronuclear single quantum coherence) 2D NMR (nuclear magnetic resonance) spectra. 'ChemoSpec2D' deploys methods aimed primarily at classification of samples and the identification of spectral features which are important in distinguishing samples from each other. Each 2D spectrum (a matrix) is treated as the unit of observation, and thus the physical sample in the spectrometer corresponds to the sample from a statistical perspective. In addition to chemometric tools, a few tools are provided for plotting 2D spectra, but these are not intended to replace the functionality typically available on the spectrometer. 'ChemoSpec2D' takes many of its cues from 'ChemoSpec' and tries to create consistent graphical output and to be very user friendly.
pfacLoadingswere incorrectly reordering their matrices.
inspectLvlswas not excluding any loading matrices when
loading = NULL.
pfacLoadingsnow check to see if the requested loading has already been computed, and if so, it is not computed again. Loadings are named
Spectra2Dobject. These functions also gain a plot argument so that plots can be suppressed if desired. These changes were made for dealing with large data sets which can occupy a lot of memory and slow down the computation of the contours. Using
plot = FALSEallows one to compute the loadings and then figure out desirable contour levels before running with
plot = TRUE.
pfacSpectra2Dgains an argument
parallel = TRUEthe parallel computational environment is automatically configured for the user. If
FALSEthe user is responsible for setting up the environment. This is useful if working on Azure or AWS EC2.
showScalenow opens a pdf document showing the scale used with
plotSpectra2Dnow chosen via
pretty()and are easier to interpret.
plotSpectra2Dgains an option for a grid aligned with the ticks.
plotScree, which works with
groupNcolormoved to non-exported functions, and re-named to
import2Dspectraextensively reworked to fix problems and allow for easy expansion in the future.
files2Spectra2DObjecttweaked a bit.
centscaleSpectra2Dand now centers and optionally scales the data.
plotSpectra2Dso that it will plot more than one spectrum.
.findNAled to code clean up (better variable names and code notes).
pfacLoadingsnow returns the modified
Spectra2Dobject, not the loadings matrix.
inspectLvlscan now access the loadings matrix, if present, in a
pfacSpectra2Dwas fixed. This task is now handled by helper function
.makeArraysince it is also required by
pfacLoadingssimplified, and some logical errors fixed.
MUD1gains some negative peaks for more comprehensive graphical tests.
.normAroundZerooverhauled, and renamed to
inspectLvlsto allow quick selection of levels.
MUD1test data set.
removePeaks2D(part of the problem was in
sumSpectra2Dnow reports the number of data points in F2 and the number of slices in F1.
chkSpectra2Ddoes a better job of checking and reporting about extra data.