NEWS.md
baselineSpectra() which prevented plots from showing in the vignette (and presumeably any report). Unfortunately also had to remove the ability to loop over the various spectra with one call to the function.cv_pcaSpectra which affected the results. Data was being row scaled internally, this was removed. Scaling was made consistent with c_pcaSpectra. Data will be centered before proceeding (notice repeated from 6.1.3 which did not go to CRAN).mclust3dSpectra was overhauled completely and now uses plotly graphics (an interactive plot appears in a browser window). The color scheme was changed to use Col12 (see ?colorSymbol).plotScoresRGL and plotScores3D have been removed from the package. Please use plot3dScores, which uses plotly, as a replacement.Spectra objects implemented. In RStudio typing SrE.IR$ will show a list of possible completions. In the R console, typing SrE.IR$ followed by the tab key shows possible completions.hmapSpectra (the plot p was not called).plotSpectra argument lab.pos can now be set to "none" to supress labeling entirely (fixes issue #88).base graphics, ggplot2 or plotly graphics:
plotSpectrasurveySpectrasurveySpectra2loopThruSpectra (which has been renamed to reviewAllSpectra)plotScree (resides in ChemoSpecUtils)plotScores (resides in ChemoSpecUtils)plotLoadings (uses patchwork and hence plotly is not relevant)plot2LoadingssPlotSpectrapcaDiagplotSampleDistaovPCAscoresaovPCAloadings (uses patchwork and hence plotly is not relevant)ggplot2 graphics output are generally similar in layout and spirit to the base graphics output, but significant improvements have been made in labeling data points using the ggrepel package. And of course the ggplot2 graphics can be modified after creation through the usual mechanisms.plotly graphics output are interactive plots which can be used for better understanding the data. plotly provides tools such as zoom, interactive labels and custom positioning which are very useful.options(ChemoSpecGraphics = "option").?GraphicsOptions.loopThruSpectra has been renamed reviewAllSpectra to better reflect what it does under the new graphics options.plotScree2 which has been deprecated for some time now, was removed.leg.loc argument now allow much more flexibility with regard to how the legend is positioned. See the documentation.plotSpectra, when using base graphics, now positions the sample names by a different mechanism, but gives a similar result.updateGroups which has been in ChemoSpecUtils for a while but effectively hidden from users of ChemoSpec.plotSpectraDist which had strange limits.mclustSpectra which had an error and used data that was not a good illustration.sampleDistSpectra was renamed sampleDist and moved to ChemoSpecUtils. The internal workings and plot details have changed.removeFreq now accepts a formula for rem.freq. The old syntax remains valid. See the documentation for ChemoSpec2D for examples of how to construct formulas.sampleDist, sampleDist.Spectra and sampleDist.Spectra2D.hypTestScores now shows several ways to look at the results.files2SpectraObject now will pass the argument SOFC to readJDX if JCAMP-DX files are being processed.hmapSpectra the return values (updated in version 5.1.48) were labeled incorrectly. Noticed by Gabriele Beltrame. The function now returns everything returned by seriation::hmap making it easier for the user to extract the information they desire. Documentation was improved, and additional examples were added illustrating how to pass arguments downstream to customize the plot.plotScores3D and plotScoresRGL in which the wrong percent variance was plotted in the axes labels. Reported by Owen Horsfall.matrix2SpectraObject can now handle multiple input matrices (i.e. argument in.file can be a vector of file names). The function now includes a progress bar, similar to files2SpectraObject.s_pcaSpectra which performs sparse PCA added.irlba_pcaSpectra which performs IRLBA PCA added.files2SpectraObject can now accept any arguments to list.files or read.table via the … mechanism. Arguments are sanitized more robustly. However, it is possible to pass arguments that may not be of real utility. For instance na.strings can be specified, but any NA in the data imported will trigger warnings and errors..groupNcolor (the problem seems to have been present from the very beginning). Reported by Reinhard Kerschner (many thanks!). Note .groupNcolor now resides in ChemoSpecUtils. Reported here for convenience.matrix2SpectraObject now uses tryCatch() to more gracefully fail and offer suggestions to user.files2SpectraObjectnews(package = "ChemoSpec").