NEWS.md

ChemoSpec2D 0.5.0 2020-10-09

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:
  • plotScores
  • plotScree

Both of these functions are actually in ChemoSpecUtils and called on behalf of the user when needed.

• 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.

Misc.

• Functions with the leg.loc argument now allow much more flexibility with regard to how the legend is positioned. See the documentation.

ChemoSpec2D 0.4.187 2020-03-15

Changes in ChemoSpecUtils that affect ChemoSpec2D

• 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 files2Spectra2DObject documentation.

Misc.

• Checked against R 4.1 RC

ChemoSpec2D 0.4.176 2020-08-30

Misc.

• Documentation (pkgdown site) is now automated via CI.
• Build & check via CI now active.

ChemoSpec2D 0.4.156 2020-03-02

Bugs Fixed

• Reporting of shifts from hats_alignSpectra2D has been corrected. Only the reporting was foobar'ed. The alignment worked fine. Defaults for plots also improved.

ChemoSpec2D 0.4.147 2020-02-18

New Features: Importing Spectra

• Format Btotxt added to import2DSpectra, allowing import of 2D data exported by the Bruker command "totxt".
• Format dx added to import2DSpectra for use with JCAMP-DX files, via package readJDX which has recently learned how to import 2D NMR data sets.
• Format F1F2RI-F1decF2dec2 added to import2DSpectra which handles the import of JEOL spectra exported as "generic ascii".
• files2Spectra2DObject gains a new argument allowSloppy. This will allow one to import data sets that do not have the same dimensions. The intent here is to deal with data sets where the number of points in each dimension is similar but not identical. This is an experimental feature, and additional functions will be needed to handle this kind of data. See the documentation for details.
• files2Spectra2DObject gains a progress bar and will now accept a path and other arguments to list.files, bringing it in line with ChemoSpec::files2SpectraObject.

New Features: Miscellaneous

• Function normSpectra2D gets a new method to scale spectra on [-1 ... 1].
• Function hats_alignSpectra2D gains new arguments dist_method and maximize which allows the user to pass their choice of distance measure through to the objective function used to evaluate the overlap of the spectra. This greatly improves the quality of the alignment. See the documentation for additional details.

New Functions

• New function computeVolume added to aid in normalizing spectra to particular chemical shift regions, which are volumes when the intensity is taken into account.
• Two new convenience functions, LofL and LofC, added to assist with overlaying multiple spectra in plotSpectra2D. LofL = "List of Levels" and LofC = "List of Colors."

Significant Changes

• The basic color scheme for contours was updated to use a perceptually consistent low/blue -> high/red scheme, based on the principles in the colorspace package. The color-handling infrastructure was also changed to allow easy introduction of different color schemes in the future, though the user cannot yet make changes on the fly.
• inspectLvls simplified and arguments changed; one can now inspect just a single spectrum or a range of spectra.
• Function calcLvls rebuilt to be more consistent and logical. Values will change slightly from previous values.

Improvements

• Tick positions for plotSpectra2D when user specifies xlim and/or ylim is much more robust. Function .computeTicks was removed as it was no longer needed.
• Tick positions for plotSlice similarly made more robust.
• Format options in import2Dspectra cleaned up (documentation and code).

Bugs avoided

• pfacSpectra2D now allows control of the number of cores in use when using parallel processing. This is to avoid multiple processes on the same shared machine each trying to use all the cores for themselves. Per suggestion by Henrik Bengtsson on Twitter.

Bugs fixed

• inspectLvls was not playing nice when argument which was a vector.
• Fixed a problem with .mapColors in which NA could be returned as a color, which results in an unexpected black contour. Now removes NA and gives a warning that the requested levels are beyond the range of the data.

Changes in ChemoSpecUtils that affect ChemoSpec2D

• New color and symbol schemes for the groups are now provided for use during the import process.

Misc.

• Documentation updates and improvement.
• Added documentation for updateGroups which has been in ChemoSpecUtils for a while but effectively hidden from users of ChemoSpec2D.
• Cleaned up some roxygen2 warnings.
• Unit test framework converted to tinytest.
• Removed robustbase from suggests (not needed).
• .makeArray gains a unit test.
• Function .rescale rebuilt to be more flexible.

ChemoSpec2D 0.3.166 2019-06-09

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, dating to the early days of ChemoSpec. Note that plotScores is actually in ChemoSpecUtils but is called from ChemoSpec2D, affecting the results here.
• Scree plots for class(mia) were plotting the eigenvalues instead of the percent variance explained.
• The computation of the loading pseudo-spectrum for class(mia) was incorrect and gave a rotated version of the correct result.

New Features

• A function to align spectra, hats_alignSpectra2D was added, along with a number of supporting functions.
• conColScheme has moved to ChemoSpecUtils and can now also handle Spectra2D objects. It is also now more user friendly.
• New function shiftSpectra2D added to permit manual shifting.
• centscaleSpectra2D gains the ability to scale by log or log10.

Significant Changes

• Data set MUD1 was completely rebuilt.
• New data set MUD2 added, for purposes of testing alignment algorithms.

Possible Breaking Changes

• centscaleSpectra2D defaults have changed.

Misc.

• Documentation colorSymbol was moved to package ChemoSpecUtils.
• Unit testing framework changed to tinytest.
• normSpectra2D now checks the input method as a valid choice.

ChemoSpec2D 0.2.55 2019-04-30

New Features

• New function popSpectra2D computes "plain old PCA" on a Spectra2D data set, using the IRLBA algorithm. The data is unstacked before PCA.

Improvements

• pfacSpectra2D now has a nfac as an argument; previously the user was warned to provide it. This is clearer, more user-friendly and more consistent with other functions.
• Small changes to several functions to work more consistently with changes in ChemoSpecUtils and ChemoSpec which introduce more PCA variants.
• miaLoadings, popLoadings (never publically released), and pfacLoadings were collapsed into plotLoadings2D.
• Improved reporting in chkSpectra.
• NAMESPACE cleaned up a bit.
• files2Spectra2DObject is now careful to remove any dimnames of the imported matrices, to avoid causing a ruckus with chkSpectra.

Deprecated Functions

• toChemoSpec was removed as popSpectra2D provides a complete workflow corresponding to unstacking, computing PCA and reassembling the loadings.

ChemoSpec2D 0.2.19 2019-02-28

Bug Fixes

• Both miaLoadings and pfacLoadings were incorrectly reordering their matrices.
• inspectLvls was not excluding any loading matrices when loading = NULL.

Improvements

• miaLoadings and pfacLoadings now check to see if the requested loading has already been computed, and if so, it is not computed again. Loadings are named Loading_x in the Spectra2D object. These functions also gain a plot argument so that plots can be suppressed if desired. These changes were made for dealing with large data sets which can occupy a lot of memory and slow down the computation of the contours. Using plot = FALSE allows one to compute the loadings and then figure out desirable contour levels before running with plot = TRUE.
• pfacSpectra2D gains an argument setup. If TRUE and parallel = TRUE the parallel computational environment is automatically configured for the user. If FALSE the user is responsible for setting up the environment. This is useful if working on Azure or AWS EC2.

ChemoSpec2D 0.2.0 2018-11-30

New Features

• Function plotSlice added.

Improvements

• Function showScale now opens a pdf document showing the scale used with plotSpectra2D.
• Improved error message from inspectLvls.
• Numerous documentation improvements, including vignette.
• Improved examples.
• Test and demo data set MUD1 rebuilt.

Bug Fixes

• Internal function .computeTicks was not detecting discontinuities in a robust manner.

Misc.

• First release to CRAN!

ChemoSpec2D 0.1.623 2018-11-09

Improvements

• plotSpectra2D now accepts xlim and ylim.
• Ticks in plotSpectra2D now chosen via pretty() and are easier to interpret.
• plotSpectra2D gains an option for a grid aligned with the ticks.

Misc.

• Consistent argument checking implemented via ChemoSpecUtils::.chkArgs.

ChemoSpec2D 0.1.532 2018-10-28

New Features

• hcaScores added via ChemoSpecUtils.

Misc.

• Checked against devel version of ChemoSpecUtils.

ChemoSpec2D 0.1.505 2018-10-20

Misc.

• Ellipses in score plots working.

ChemoSpec2D 0.1.471 2018-10-03

Misc.

• Improved documentation.
• Modifications to work with ChemoSpecUtils.

ChemoSpec2D 0.1.458 2018-08-07

New Features

• Added function plotScree, which works with miaSpectra2D.
• Added miaLoadings.

ChemoSpec2D 0.1.451 2018-08-30

Improvements

• groupNcolor moved to non-exported functions, and re-named to .groupNcolors.
• import2Dspectra extensively reworked to fix problems and allow for easy expansion in the future.
• files2Spectra2DObject tweaked a bit.
• centerSpectra2D becomes centscaleSpectra2D and now centers and optionally scales the data.

ChemoSpec2D 0.1.434 2018-08-20

Misc.

• Vignette updated.

ChemoSpec2D 0.1.431 2018-08-19

Improvements

• Modified plotSpectra2D so that it will plot more than one spectrum.

ChemoSpec2D 0.1.419 2018-08-18

Misc.

• Added unit tests for .findNA.
• Setting up unit tests for .findNA led to code clean up (better variable names and code notes).
• Added unit tests for centerSpectra2D.
• Added unit tests for chkSpectra2D.

ChemoSpec2D 0.1.412 2018-08-17

Misc.

• pfacLoadings now returns the modified Spectra2D object, not the loadings matrix.
• inspectLvls can now access the loadings matrix, if present, in a Spectra2D object.

ChemoSpec2D 0.1.407 2018-08-16

New Features

• A simple means of drawing a separate scale/legend for the contour plots was added.

Bug Fixes

• An error in the construction of the data cube / array in pfacSpectra2D was fixed. This task is now handled by helper function .makeArray since it is also required by centerSpectra2D.

Misc.

• pfacLoadings simplified, and some logical errors fixed.

ChemoSpec2D 0.1.373 2018-08-15

Misc.

• MUD1 gains some negative peaks for more comprehensive graphical tests.
• .mapColors overhauled.
• .plotEngine overhauled.
• .normAroundZero overhauled, and renamed to .symAroundZero.
• Added convenience function inspectLvls to allow quick selection of levels.

ChemoSpec2D 0.1.328 2018-08-12

New Features

• Added centerSpectra2D function.

Misc.

• Improved MUD1 test data set.

ChemoSpec2D 0.1.314 2018-08-07

Bug Fixes

• Fixed incorrectly reversed F1 frequency removal in removePeaks2D.
• Fixed a problem with where the gray "no data" lines were drawn in removePeaks2D (part of the problem was in .findNA).

Improvements

• sumSpectra2D now reports the number of data points in F2 and the number of slices in F1.
• chkSpectra2D does a better job of checking and reporting about extra data.

Misc.

• Lots of documentation polishing.

ChemoSpec2D 0.1.295 2018-08-06

Misc.

• Rebuilt under latest R and updated packages.

ChemoSpec2D 0.0.0 2017-09-06

Misc.

• Package development begins with a port of relevant ChemoSpec materials.
• No NEWS entries until we have an initial framework in decent shape.