ChemoSpec 6.1.10 2024-02-03
Bug Fix
- Fixed a logic error in
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.
Misc.
- Package
clusterCrit is back on CRAN so it was returned to ChemoSpec.
- Misc documentation format fixes caught by CRAN.
- Remove use of
aaply and arrange to avoid dependence on plyr.
ChemoSpec 6.1.9 2023-06-06
Misc.
- Fixed a problem with unit tests that should have been run only at home that were being run at CRAN.
ChemoSpec 6.1.8 2023-06-03
Misc.
- Bumped version at the request of CRAN.
- Replaced use of
@template in documentation with inline functions, as @template is deprecated.
- There was no official 6.1.7 version, it got bogged down at CRAN.
ChemoSpec 6.1.6 2023-04-20
Misc.
- Package
clusterCrit was archived by CRAN, and hence was removed from ChemoSpec. Affects evalClusters function.
- Stopped exporting internal functions from
ChemoSpec and stopped re-exporting internal functions from ChemoSpecUtils, due to closer checking by CRAN.
- Not released to CRAN.
ChemoSpec 6.1.4 2022-10-21
Bug Fixes
- Fixed an ancient bug in
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).
New Features
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).
New Functions
averageReplicates will average sample replicates and return a new Spectra object
Misc.
- Removed remaining deprecation warnings about
plotScoresRGL and plotScores3D.
- Removed
loopThroughSpectra which was “sort of” deprecated. Use reviewAllSpectra instead.
normSpectra documentation updated to include warning about protein-containing samples and the PQN method.
ChemoSpec 6.1.3 2022-08-06
Misc.
- This version not on CRAN.
Bug Fixes
- Fixed an ancient bug in
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.
New Features
baselineSpectra gains a new argument show to allow control of which spectra are shown to the user after baseline correction.
ChemoSpec 6.1.2 2022-02-08
Misc.
- Removed stale entries in
Suggests and Imports - housekeeping for CRAN, no user-facing changes.
ChemoSpec 6.1.0 2022-01-08
Overhauled Functions
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).
Defunct Functions
- Functions
plotScoresRGL and plotScores3D have been removed from the package. Please use plot3dScores, which uses plotly, as a replacement.
New Features
- Tab completion for
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.
Misc.
- Fixed the example in
hmapSpectra (the plot p was not called).
plotSpectra argument lab.pos can now be set to "none" to supress labeling entirely (fixes issue #88).
ChemoSpec 6.0.1 2021-10-09
Significant Changes to Graphics Output
- 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.
Misc.
plotScree2 which has been deprecated for some time now, was removed.- Functions with the
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.
ChemoSpec 5.3.21 2021-07-05
Misc.
- Update
hmapSpectra as the wrapped function in seriation has changed.
ChemoSpec 5.3.11 2021-03-24
Changes in ChemoSpecUtils that affect ChemoSpec
- Documentation of
... in sumSpectra corrected to show how to pass tol to check4Gaps.
- Option to use
Col7 a palette of 7 colorblind-friendly colors added to files2SpectraObject documentation.
Misc.
- Checked against
R 4.04 RC
ChemoSpec 5.3.2 2020-08-09
Misc.
- Vignettes updated, and moved to html format.
- Continuous integration for building and checking, as well as automated building of the
pkgdown documentation site.
- The “Reference Spectrum” panel label in
plotLoadings shortened to “Ref. Spectrum” in order to fit the allotted space better.
ChemoSpec 5.2.12 2020-01-23
Misc.
- Fixed class-checking issues due to changes coming in R 4.0 coming soon.
- Improved documentation in various places.
- Added documentation for
updateGroups which has been in ChemoSpecUtils for a while but effectively hidden from users of ChemoSpec.
- Fixed the example in
plotSpectraDist which had strange limits.
- Fixed the example in
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.
Changes in ChemoSpecUtils that affect ChemoSpec
- New color and symbol schemes are now provided for using during the import process.
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.- New functions
sampleDist, sampleDist.Spectra and sampleDist.Spectra2D.
ChemoSpec 5.1.88 2019-11-14
Improvements
- Documentation for
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.
Bug Fixes
- In
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.
- Fixed a bug in
plotScores3D and plotScoresRGL in which the wrong percent variance was plotted in the axes labels. Reported by Owen Horsfall.
ChemoSpec 5.1.48 2019-07-25
Improvements
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.
New Features
- A new vignette, Introduction to PCA, was added.
ChemoSpec 5.1.34 2019-06-23
Improvements
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.
Bug Fixes
- Fixed a buglet in
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".
Misc.
- Unit test framework shifted to
tinytest.
- Additional unit tests added.
ChemoSpec 5.1.9 2019-06-09
New Features
- Function
s_pcaSpectra which performs sparse PCA added.
- Function
irlba_pcaSpectra which performs IRLBA PCA added.
Improvements
- Numerous internal changes to the handling of PCA results were made to accommodate the introduction of sparse PCA features, and allow for easier future introduction of other PCA methods.
Bug Fixes
- An issue with the setting of x and y limits in
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.
Misc.
- Function
conColScheme moved to package ChemoSpecUtils.
- Documentation
colorSymbol was moved to package ChemoSpecUtils.
- Vignette updated regarding color issues.
ChemoSpec 5.0.229 2019-02-28
Misc.
- Unit tests added for
.cleanArgs.
ChemoSpec 5.0.215 2018-12-06
Improvements
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.
Misc.
plotScree added to r_pcaSpectra example.
ChemoSpec 5.0.207 2018-11-28
Improvements
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!).
ChemoSpec 5.0.193 2018-11-20
Bug Fixes
- Fixed a problem with color assignment in
.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.
Improvements
matrix2SpectraObject now uses tryCatch() to more gracefully fail and offer suggestions to user.files2SpectraObject
Notices