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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).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.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").These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.