Skip to contents

Changelog

Source: NEWS.md

chromatographR 0.6.0

New features
  • Enabled use of parallel package for parallel processing (in addition to current options using mcapply). (These options require the installation of suggested package pbapply).
  • Updated get_peaktable for greater flexibility (e.g. for usage of ‘Chemstation’ peak lists as input).
Other changes
  • Made some minor changes to vignette to improve clarity (e.g. using single wavelength for integration, etc.)
Bug fixes
  • Fixed error in attach_metadata when there are NA values in merge column.

chromatographR 0.5.6

  • Fixed bug in preprocess function causing fatal error due to misrecognition of matrices.
  • Fixed behavior of plot_chroms and correct_rt to allow automatic detection of lambda for 1D chromatograms.
  • Fixed bug in combine_peaks (due to misplaced parenthesis).
  • Added new option to filter by maximum peak area or height in filter_peaktable (what = "max"), as suggested by Katherine Holmes.

chromatographR 0.5.5

  • Fixed bug in get_peaktable causing failure to print strip plot when plot_it == TRUE.

chromatographR 0.5.4

  • Added .zenodo.json file.

chromatographR 0.5.3

  • Fixed bug in plot_chroms causing mismatched legend labels in base R plot.
  • Added additional arguments to plot_chroms function: xlim,ylim, and legend_position.
  • Added additional information about arguments available in get_peaks for fine-tuning the peak-finding algorithm (in response to #27).

chromatographR 0.5.2

  • Added metadata argument to reshape_peaktable for filtering metadata fields.
  • Added option for renaming peaks via reshape_peaktable by providing a named character vector.

chromatographR 0.5.1

  • In plot_chroms, show_legend now defaults to FALSE to prevent overloading of the plot.
Bug fixes
  • Fixed syntactical bug in get_peaktable when applied to gaussian peak list.
  • Fixed bug caused by improper transfer of time.units metadata by filter_peaks function.
  • Added default for missing time.units in plot.peak_list.

chromatographR 0.5.0

New features
  • Added ggplot2 option to plot_spectrum, plot.peak_table and plot_all_spectra functions.
  • Reworked write_chroms for more sensible handling of paths and added filename argument.
  • Updated get_purity function to improve speed.
  • Added additional argument to reshape_chroms function for subsetting data by retention times (rts).
  • Added parallel processing through the pbapply package for the correct_rt, get_peaks, and preprocess functions by setting the cl argument.
Other changes
  • Changed behavior of preprocess when inferring retention times so chromatograms are no longer rounded down to the largest integer.
  • In preprocess, spectral smoothing is no longer applied on 2D chromatograms, removing error message when preprocess is used with default settings.
  • Moved position of ... argument to end in plot.peak_table.
  • Changed progress_bar argument to show_progress in correct_rt, preprocess and get_peaks to fix strange pmatch behavior with additional arguments to preprocess.
  • Changed orientation of “plotly” plots generated by plot_spectrum to match other plotting engines.
  • Deprecated the mc.cores argument in correct_rt is now deprecated in favor of the new cl argument.
  • Deprecated the parallel argument in preprocess in favor of just using cl.
  • Changed name of first argument in mirror_plot from peak_table to x. Otherwise the function has not changed.
  • Added additional tests, improving test coverage to 80%.
  • Updated get_chrom_list (internal) to allow parsing of subsetted lists.

chromatographR 0.4.8

  • Fixed bug in merge_peaks function so it works properly (to combine 2 or more peaks in a peak table).
  • Fixed bugs in plot_chroms preventing plotting with ggplot2 and plotting wrong chromatograms in base R.
  • Added additional tests for plot_chroms and reshape functions.

chromatographR 0.4.7

  • Added reshape_peaktable function for conversion of peak tables to long format.
  • Turned off estimate_purity in get_peaks function by default.
  • Added option to filter by wavelength in reshape_chroms, speeding up plot_chroms.

chromatographR 0.4.6

New Features

  • Added plot_chroms function for easily plotting multiple traces from a list of chromatograms.
  • Minor changes to internal syntax of correct_rt to give more informative error messages.
  • Added estimate_purity argument in get_peaks to toggle peak purity estimation.
  • Changed default setting for progress_bar in correct_rt and get_peaks. Now defaults to TRUE if pbapply is installed.
  • Added additional tests of utility functions and new plot_chroms function.
  • Minor changes to vignette.
  • Minor changes to documentation.

Bug fixes

  • Fixed bug causing mismatched time axes and alignment issues after VPdtw warping (again), so that it returns matrices with a consistent time axis.
  • Fixed y unit label in boxplot.peak_table function.
  • Fixed behavior of plot_spectrum so spectrum is exported properly when engine == plotly.
  • Fixed bug in write_peaktable when writing to xlsx.

chromatographR 0.4.5

New Features

  • Added reshape_chroms function for converting chromatograms to “long” format.
  • Added write_peaktable function to easily write peak_table to csv or xlsx.
  • Added get_purity function for assessing peak purity.
  • Allow multiple peaks as arguments to plot.peaktable.
  • Added functions for plotting traces and spectra with plotly: plotly_trace and plotly_spec.
  • Fixed preprocess so it will no longer try to interpolate along columns for 2D data.
  • Added stand-alone boxplot function for peak_table objects.
  • Added a new class (ptw_list) and plotting function for lists of ptw alignment objects.
  • Added plot_it argument in correct_rt for plotting alignments.
  • Added VPdtw as a dependency (instead of being only suggested).
  • Added progress_bar option to get_peaks and correct_rt.
  • Improved error handling in plot.peaklist.
  • Updated find_peaks function with more and better smoothing options to improve peak-finding. Now defaults to gaussian smoothing.
  • Changed fit_peaks function and syntax (see below).
  • Minor updates to vignette.
Changes to fit_peaks function:
  • Simplified logic in fit_peaks function.
  • Modified fit_peaks syntax so it now takes a matrix (x) and a wavelength (lambda) instead of a numeric vector (y).
  • Incorporated assessment of peak purity during peak fitting.
  • Added wavelength (lambda) to peak_list and peak_table metadata.
  • Fixed bug to allow fitting of a single peak with fit_peaks.

Bug fixes

  • Fixed bug causing mismatched time axes (and improper alignment of chromatograms) after variable penalty dynamic time warping (VPdtw).
  • Fixed bug in attach_metadata that could result in disordered rows.
  • Fixed occasional test failure on MKL server by skipping cluster_spectra test on CRAN.
  • Adjusted cluster_spectra and combine_peaks functions so messages can be suppressed with verbose == FALSE.

chromatographR 0.4.4

CRAN release: 2022-08-24

  • Fixed issue with tests when run on certain machines (MKL).

chromatographR 0.4.3

CRAN release: 2022-08-22

  • Minor changes to documentation.
  • Added additional check of chrom_list dimensions and names.

chromatographR 0.4.2

New features
  • Added option to select time.units for peak area in get_peaks function facilitating better comparison with vendor software.
  • Now allow preservation of instrumental metadata through pre-processing and alignment steps.
  • Added filter_peaktable function.
Minor changes:
  • Deprecated load_chroms function. Please use read_chroms from chromConverter to import files instead.
  • Changed default behavior in correct_rt to corrected_values rather than models.
  • Added more informative warnings and error messages to various functions.
  • Now recommend installation of VPdtw from CRAN instead of https://ethanbass.github.io/drat/
  • Fixed typos in vignette
Bug fixes
  • Fixed bug in cluster_spectra affecting peaks with 0 standard deviation.
  • Fixed bug affecting peak_list metadata.

chromatographR 0.4.1

CRAN release: 2022-05-19

  • Extended package DESCRIPTION and added citations to relevant references.
  • Added \value and \section{Side effects} fields to docs for the various plot functions.
  • Fixed bug in mirror_plot so legend can be fully hidden by setting plot_legend to FALSE.
  • Fixed bug in scan_chrom so additional arguments are passed to plot_spectrum.
  • Added color argument to customize color of fitted peaks in plot.peak_list.
  • Fixed plot functions and examples so they don’t change par settings.
  • Other small updates to documents (mostly formatting or small clarifications).
  • Fixed plot.peak_table so it can return spectra if export_spectrum is TRUE.
  • Added error for box_plot option in plot.peak_table if metadata is not attached.
  • Added error for box_plot option in plot.peak_table if peak is not provided to loc.
  • Added error in plot_spectrum function for user-supplied retention times beyond the edges of the chromatogram.
  • Added error in plot_spectrum function for unspecified lambda (if what=="click).
  • Released on CRAN

chromatographR 0.4.0

  • Added support for variable penalty dynamic time warping (VPdtw) through correct_rt function.
  • Fixed bug in get_peaks function.
  • Allow preprocessing without interpolation.
  • Fixed bug so preprocess can work on Windows (without parallel processing).
  • Allow use of raw data for peak integration in get_peaks.
  • Added verbose option to correct_rt to print reference chromatogram.

chromatographR 0.3.0

  • Added a NEWS.md file to track changes to the package.