ethanbass/chromatographR: v0.5.0

Published May 7, 2023 | Version v0.5.0

Software Open

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.
In plot_chroms, show_legend now defaults to false.
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.

Files

Name	Size	Download all
ethanbass/chromatographR-v0.5.0.zip md5:4c9eb7a2dd5f1a79a4392f5e0e0c2920	2.7 MB	Preview Download

Is supplement to: https://github.com/ethanbass/chromatographR/tree/v0.5.0 (URL)