chromatographR 0.4.5
New features
- Fixed bug causing mismatched time axes (and improper alignment of chromatograms) after variable penalty dynamic time warping (VPdtw).
- Added
reshape_chroms
function for converting chromatograms to “long” format. - Added
export.peaktable
function to easily write peak_table tocsv
orxlsx
. - 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
andplotly_spec
. - Fixed
preprocess
so it will no longer try to interpolate along columns for 2D data. - Added stand-alone
boxplot
function forpeak_table
objects. - Fixed bug in
attach_metadata
that could result in disordered rows. - Changed
fit_peaks
function and syntax (see below). - Added a new class (
ptw_list
) and plotting function for lists ofptw
alignment objects. - Added
plot_it
argument incorrect_rt
for plotting alignments. - Added VPdtw as a dependency (instead of being only suggested).
- Adjusted
cluster_spectra
andcombine_peaks
functions so messages can be suppressed withverbose == FALSE
. - Fixed occasional test failure on MKL server by skipping
cluster_spectra
test on CRAN. - Updated find_peaks function with more and better smoothing options. The defaults smoothing is slightly changed. Find peaks will now do gaussian smoothing by default with
- Added
progress_bar
option toget_peaks
andcorrect_rt
. - Improved error handling in
plot.peaklist
. - 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
) topeak_list
andpeak_table
metadata. - Fixed bug to allow fitting of a single peak with
fit_peaks
.
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 inget_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 useread_chroms
from chromConverter to import files instead. - Changed default behavior in
correct_rt
tocorrected_values
rather thanmodels
. - 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
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 settingplot_legend
to FALSE. - Fixed bug in
scan_chrom
so additional arguments are passed toplot_spectrum
. - Added
color
argument to customize color of fitted peaks inplot.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 ifexport_spectrum
is TRUE. - Added error for
box_plot
option inplot.peak_table
if metadata is not attached. - Added error for
box_plot
option inplot.peak_table
if peak is not provided toloc
. - Added error in
plot_spectrum
function for user-supplied retention times beyond the edges of the chromatogram. - Added error in
plot_spectrum
function for unspecifiedlambda
(ifwhat=="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 tocorrect_rt
to print reference chromatogram.