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.clusterCrit is back on CRAN so it was returned to ChemoSpec.aaply and arrange to avoid dependence on plyr.@template in documentation with inline functions, as @template is deprecated.clusterCrit was archived by CRAN, and hence was removed from ChemoSpec. Affects evalClusters function.ChemoSpec and stopped re-exporting internal functions from ChemoSpecUtils, due to closer checking by CRAN.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).baselineSpectra gains a new argument show to allow control of which spectra are shown to the user after baseline correction (notice repeated from 6.1.3 which did not go to CRAN).averageReplicates will average sample replicates and return a new Spectra objectplotScoresRGL and plotScores3D.loopThroughSpectra which was "sort of" deprecated. Use reviewAllSpectra instead.normSpectra documentation updated to include warning about protein-containing samples and the PQN method.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.baselineSpectra gains a new argument show to allow control of which spectra are shown to the user after baseline correction.Suggests and Imports - housekeeping for CRAN, no user-facing changes.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).Courtesy GSOC and Tejasvi Gupta, the following plotting functions gain the ability to produce either 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)The 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.
The 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.
The graphics output options can be chosen by options(ChemoSpecGraphics = "option").
See the details in new help file ?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.hmapSpectra as the wrapped function in seriation has changed.... in sumSpectra corrected to show how to pass tol to check4Gaps.Col7 a palette of 7 colorblind-friendly colors added to files2SpectraObject documentation.R 4.04 RCpkgdown documentation site.plotLoadings shortened to "Ref. Spectrum" in order to fit the allotted space better.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.plotScoresRGL gains an argument axes which allows one to control the drawing of the reference axes.hmapSpectra now returns the carpet matrix in addition to the sample and frequency rankings.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.hcaSpectra that involved an undesirable cast to data frame, which upset the cosine calculation.evalClusters was not returning the result in the case of pkg = "NbClust".tinytest.s_pcaSpectra which performs sparse PCA added.irlba_pcaSpectra which performs IRLBA PCA added.plotScores was fixed. This was a long standing bug that somehow escaped notice from the early days of this package. Note that plotScores is actually in ChemoSpecUtils but is called from ChemoSpec, affecting the results here.conColScheme moved to package ChemoSpecUtils.colorSymbol was moved to package ChemoSpecUtils..cleanArgs.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.plotScree added to r_pcaSpectra example.files2SpectraObject can now accept optional arguments path and recursive to allow reading through a directory substructure. In addition, a progress bar is now displayed unless debug = TRUE. Both features suggested by Reinhard Kerschner along with preliminary code (thanks!)..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").