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.
miaLoadings and pfacLoadings were incorrectly reordering their matrices.inspectLvls was not excluding any loading matrices when loading = NULL.miaLoadings and pfacLoadings now check to see if the requested loading has already been computed, and if so, it is not computed again. Loadings are named Loading_x in the Spectra2D object. 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 = FALSE allows one to compute the loadings and then figure out desirable contour levels before running with plot = TRUE.pfacSpectra2D gains an argument setup. If TRUE and parallel = TRUE the parallel computational environment is automatically configured for the user. If FALSE the user is responsible for setting up the environment. This is useful if working on Azure or AWS EC2.plotSlice added.showScale now opens a pdf document showing the scale used with plotSpectra2D.inspectLvls.MUD1 rebuilt.plotSpectra2D now accepts xlim and ylim.plotSpectra2D now chosen via pretty() and are easier to interpret.plotSpectra2D gains an option for a grid aligned with the ticks.ChemoSpecUtils::.chkArgs.hcaScores added via ChemoSpecUtils.ChemoSpecUtils.ChemoSpecUtils.plotScree, which works with miaSpectra2D.miaLoadings.groupNcolor moved to non-exported functions, and re-named to .groupNcolors.import2Dspectra extensively reworked to fix problems and allow for easy expansion in the future.files2Spectra2DObject tweaked a bit.centscaleSpectra2D and now centers and optionally scales the data.plotSpectra2D so that it will plot more than one spectrum..findNA..findNA led to code clean up (better variable names and code notes).centerSpectra2D.chkSpectra2D.pfacLoadings now returns the modified Spectra2D object, not the loadings matrix.inspectLvls can now access the loadings matrix, if present, in a Spectra2D object.pfacSpectra2D was fixed. This task is now handled by helper function .makeArray since it is also required by centerSpectra2D.pfacLoadings simplified, and some logical errors fixed.MUD1 gains some negative peaks for more comprehensive graphical tests..mapColors overhauled..plotEngine overhauled..normAroundZero overhauled, and renamed to .symAroundZero.inspectLvls to allow quick selection of levels.centerSpectra2D function.MUD1 test data set.removePeaks2D.removePeaks2D (part of the problem was in .findNA).sumSpectra2D now reports the number of data points in F2 and the number of slices in F1.chkSpectra2D does a better job of checking and reporting about extra data.ChemoSpec materials.