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