mclust3dSpectrawas overhauled completely and now uses
plotlygraphics (an interactive plot appears in a browser window). The color scheme was changed to use
plotScores3Dhave been removed from the package. Please use
plot3dScores, which uses
plotly, as a replacement.
Spectraobjects implemented. In RStudio typing
SrE.IR$will show a list of possible completions. In the
SrE.IR$followed by the tab key shows possible completions.
pwas not called).
lab.poscan now be set to
"none"to supress labeling entirely (fixes issue #88).
loopThruSpectra(which has been renamed to
plotlyis not relevant)
plotlyis not relevant)
ggplot2graphics output are generally similar in layout and spirit to the
basegraphics output, but significant improvements have been made in labeling data points using the
ggrepelpackage. And of course the
ggplot2graphics can be modified after creation through the usual mechanisms.
plotlygraphics output are interactive plots which can be used for better understanding the data.
plotlyprovides tools such as zoom, interactive labels and custom positioning which are very useful.
options(ChemoSpecGraphics = "option").
loopThruSpectrahas been renamed
reviewAllSpectrato better reflect what it does under the new graphics options.
plotScree2which has been deprecated for some time now, was removed.
leg.locargument now allow much more flexibility with regard to how the legend is positioned. See the documentation.
plotSpectra, when using
basegraphics, now positions the sample names by a different mechanism, but gives a similar result.
sumSpectracorrected to show how to pass
Col7a palette of 7 colorblind-friendly colors added to
updateGroupswhich has been in
ChemoSpecUtilsfor a while but effectively hidden from users of
plotSpectraDistwhich had strange limits.
mclustSpectrawhich had an error and used data that was not a good illustration.
sampleDistand moved to
ChemoSpecUtils. The internal workings and plot details have changed.
removeFreqnow accepts a formula for
rem.freq. The old syntax remains valid. See the documentation for
ChemoSpec2Dfor examples of how to construct formulas.
hypTestScoresnow shows several ways to look at the results.
files2SpectraObjectnow will pass the argument
readJDXif JCAMP-DX files are being processed.
hmapSpectrathe return values (updated in version 5.1.48) were labeled incorrectly. Noticed by Gabriele Beltrame. The function now returns everything returned by
seriation::hmapmaking 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.
plotScoresRGLin which the wrong percent variance was plotted in the axes labels. Reported by Owen Horsfall.
plotScoresRGLgains an argument
axeswhich allows one to control the drawing of the reference axes.
hmapSpectranow returns the carpet matrix in addition to the sample and frequency rankings.
matrix2SpectraObjectcan now handle multiple input matrices (i.e. argument
in.filecan be a vector of file names). The function now includes a progress bar, similar to
hcaSpectrathat involved an undesirable cast to data frame, which upset the cosine calculation.
evalClusterswas not returning the result in the case of
pkg = "NbClust".
s_pcaSpectrawhich performs sparse PCA added.
irlba_pcaSpectrawhich performs IRLBA PCA added.
plotScoreswas fixed. This was a long standing bug that somehow escaped notice from the early days of this package. Note that
plotScoresis actually in
ChemoSpecUtilsbut is called from
ChemoSpec, affecting the results here.
files2SpectraObjectcan now accept any arguments to
read.tablevia the … mechanism. Arguments are sanitized more robustly. However, it is possible to pass arguments that may not be of real utility. For instance
na.stringscan be specified, but any
NAin 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
.groupNcolornow resides in
ChemoSpecUtils. Reported here for convenience.
tryCatch()to more gracefully fail and offer suggestions to user.
news(package = "ChemoSpec").