Changelog

Source: NEWS.md

chromatographR 0.7.4

• Added new heatmap plot in plot_chroms.
• Added labeling of spectral peaks for ggplot2 and plotly plots in plot_spectrum.
• Added minimum amplitude for labeling of spectral peaks in plot_spectrum. Peaks are now labeled only if they exceed 5% of the maximum signal intensity.
• Removed parallel and mc.cores argument from preprocess (deprecated in v0.5.0).
• Added title argument in plot_chroms.
• Added option for different plotting engines through engine argument in plot.ptw_list.
• Added option for heatmap plots through what argument in plot.ptw_list.
• Changed behavior of reshape_chroms such that it can be applied to 2D chromatograms without throwing an error.
• Added index of functions to package documentation.
• Made minor updates to documentation of functions.

Changes to GC-FID vignette

• Changed alignment plots to heatmaps rather than traces.
• Hid ggordiplot function in “folded” code block
• Added alt text to images.
• Updated call to adonis2 in accordance with new defaults in vegan v2.7-0.
• Made other minor changes to text.

Changes to chromatographR vignette

• Added explanatory figure captions.
• Added figure demonstrating comparison of alignments with new plot_chroms_heatmap function.

chromatographR 0.7.3

• Updated reshape_peaktable function to include wavelength and retention time data.
• Updated pk_tab data file to latest peak table format.
• Fixed minor issues with roxygen formatting.
• Added functional “families”.
• Fixed bug in get_peaks causing occasional errors due to edge cases.
• Added titles for ggplot2 and plotly plot_spectrum plots.
• Fixed bug in console output when providing chromatogram index as string to plot_spectrum.
• Changed default ggplot2 theme to theme_light.

chromatographR 0.7.2

• Export get_times and get_lambdas functions.
• Small revisions to documentation.
• Use tryCatch to allow for missing spectra in plot_all_spectra.
• Fixed rounding of p-values in cluster_spectra.
• Changed alpha in cluster_peaks to match common usage, such that the alpha parameter now specifies the significance level rather than the confidence level (1-alpha).
• Deprecated peak_no argument in cluster_peaks in favor of new min_size and max_size arguments.

chromatographR 0.7.1

• Fixed bug in get_peaks causing peaks to erroneously filtered out in some cases.
• Made small updates to documentation (in preprocess and fit_peaks functions) to better describe arguments.
• Added warning in mirror_plot when var contains more than two levels and levels aren’t specified.
• Fixed bug to allow mirror_plot to work properly with 2D data.
• Return dimnames for 1D ptw model objects returned by correct_rt.
• Minor updates to vignette.

chromatographR 0.7.0

• Updated correct_peaks function so it works properly for correcting retention times in peak lists.
• Added fixed_levels argument to reshape_peaktable so features can be plotted in the order they’re provided by the user.
• Added option for summing split peaks using the merge_peaks function by selecting method = "sum".
• Updated get_peaktable so that the use.cor argument works correctly (to use corrected retention times stored in a separate column).
• Fixed mirror_plot so it can take numeric input for lambdas.
• Changed default setting of verbose argument in correct_rt from FALSE to default setting.
• Removed load_chroms function. Use read_chroms instead.
• Eliminated spurious warning from attach_ref_spectra function.
• Changed name of index argument in plot.peak_list to idx. The original argument is now deprecated.
• Fixed bug affecting plot_purity argument in plot.peak_list.
• Fixed bug in reshape_chroms so empty metadata column no longer appears.
• The plot_spectrum function now includes the peak names when plotting spectra.
• Fixed correct_rt so it no longer requires user-provided lambdas for 1D chromatograms.
• Added subset.peak_table function for easily subsetting peak_tables (e.g. to exclude specific peaks or samples).
• Added what argument for plot_all_spectra (e.g. to plot multiple spectra at a particular retention time).

Refactoring of cluster_spectra function:

• For simplicity, cluster_spectra now requires reference spectra to be attached to peak table.
• Accordingly, the chrom_list argument is no longer needed.
• Saving to RDS is now turned off by default.
• The pvclust package is now suggested instead of being required.

Updates to vignette and documentation

• Suggest numeric input to lambdas instead of character input to reduce unnecessary confusion.
• Made other minor changes to text of vignette to (hopefully) improve clarity.
• Added a short section on the attachment of reference spectra.

chromatographR 0.6.1

• Fixed bug in plot functions (e.g. plot_chroms and plot_spectrum) causing error when retention times are inconsistent between chromatograms.
• Eliminated spurious warning in preprocess function.
• Updated read_chroms syntax in vignette.

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.