Exploratory Chemometrics for 2D Spectroscopy

A collection of functions for exploratory chemometrics of 2D spectroscopic data sets such as COSY (correlated spectroscopy) and HSQC (heteronuclear single quantum coherence) 2D NMR (nuclear magnetic resonance) spectra. 'ChemoSpec2D' deploys methods aimed primarily at classification of samples and the identification of spectral features which are important in distinguishing samples from each other. Each 2D spectrum (a matrix) is treated as the unit of observation, and thus the physical sample in the spectrometer corresponds to the sample from a statistical perspective. In addition to chemometric tools, a few tools are provided for plotting 2D spectra, but these are not intended to replace the functionality typically available on the spectrometer. 'ChemoSpec2D' takes many of its cues from 'ChemoSpec' and tries to create consistent graphical output and to be very user friendly.


News

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.

Reference manual

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install.packages("ChemoSpec2D")

0.2.19 by Bryan A. Hanson, 2 months ago


https://github.com/bryanhanson/ChemoSpec2D


Report a bug at https://github.com/bryanhanson/ChemoSpec2D/issues


Browse source code at https://github.com/cran/ChemoSpec2D


Authors: Bryan A. Hanson [aut, cre]


Documentation:   PDF Manual  


Task views: Chemometrics and Computational Physics


GPL-3 license


Imports R.utils, tools, utils, plyr, ThreeWay, multiway, matrixStats

Depends on ChemoSpecUtils

Suggests knitr, testthat


Suggested by ChemoSpecUtils.


See at CRAN