Changes in version 1.29.2 (2023-04-18) o replace the error message in shinyCircos test Changes in version 1.29.1 (2022-11-23) o replace aes_string by aes since aes_string is deprecated in newest ggplot2 version Changes in version 1.27.2 (2022-10-19) o use Spectra from Spectra for spectral representation instead of MSpectra from MSnbase o remove compare_Spectra and normalizeddotproduct functions and use compareSpectra from Spectra package o change vignette from Rnw to Rmd Changes in version 1.27.1 (2022-10-12) o add ShinyApps in biocViews Changes in version 1.19.0 (2020-07-02) o adapt to changes in MSnbase (renaming of Spectra to MSpectra) Changes in version 1.17.0 (2020-01-14) o change unit tests to testthat o change color 1:4 to colour character vector Changes in version 1.15.2 (2019-09-09) o add codecov o add Travis-CI for continuous integration o add CITATION file Changes in version 1.15.1 (2019-08-29) o add ggplot2 in dependencies o change GPL-2 to GPL-3 license Changes in version 1.15.0 (2019-04-23) o implement the MSnbase Spectra/Spectrum2 as the container for MS2 spectra, change all functions that they accept Spectra objects o write function convertMsp2Spectra that converts MSP files to Spectra files o change data files: change convertMSP2MSP.RData to convertMsp2Spectra, create spectra.RData, update similarityMat.RData o remove data files: binnedMSP.RData, idMSMStoMSP.RData Changes in version 1.13.1 (2019-04-04) o check if package passes R CMD build and R CMD check without any error messages and vignette can be run without any errors Changes in version 1.11.1 (2018-10-22) o adjust NEWS file to new format according to ?news: o entries are grouped according to version, with version header 'Changes in version' at the beginning of a line, followed by a version number, optionally followed by an ISO 8601 format date, possibly parenthesized o entries may be grouped according to category, with a category header (different from a version header) starting at the beginning of a line o entries are written as itemize-type lists, using one of o, *, - or + as item tag. Entries must be indented, and ideally use a common indentation for the item texts Changes in version 1.11.0 (2018-10-15) o remove Makefile from directory vignettes/ o check if package passes R CMD build and R CMD check without any error messages and vignette can be run without any errors Changes in version 1.9.0 (2018-04-16) o no changes, check if package passes R CMD build and R CMD check without any error messages and vignette can be run without any errors Changes in version 1.7.0 (2017-11-14) o implement calculation for parameter m = 0 in NDP Changes in version 1.5.0 (2017-10-20) o no changes, check if package passes R CMD build and R CMD check without any error messages and vignette can be run without any errors Changes in version 1.1.6 (2017-06-05) o correct bug fix for msp binning when there is only one entry for msp entry o improve function binning when there is only one fragment Changes in version 1.1.5 (2017-04-03) o extend unit tests for shinyApp, plottingFunctions and convert2MSP Changes in version 1.1.4 (2017-01-28) o change MSP class, create slots mz, rt, names, classes, information and adduct o add tabPanels in shinyCircos (Main, Appearance) o rearrange position of legend, implement option to show/not show legend o rescale plot when changing window size, allow for further scaling/descaling of the plot o adjust convertMSP2MSP to new class MSP, create unit tests o include msp2msp matrix, a test data set for convertMSP2MSP o set methods for names, classes, adduct and information o change the interactive shinyCircos such that the user can update the annotation data of an MSP object (name, class, information and adduct ion information) Changes in version 1.1.3 (2016-12-05) o use new email adress o use option to calculate MSP-object from msp-file directly Changes in version 1.1.2 (2016-11-17) o use absolute masses when calculating similarities in createSimilarityMatrix (bug fix) o add option links in highlight, i.e. should links be plotted or not? Changes in version 1.1.1 (2016-11-04) o change slider input as such that one is able to select a lower and lower bound instead of only a lower bound Changes in version 0.99.6 (2016-10-10) o improve allocation of clicked features in shinyCircos o change line width and colour in plotCircos Changes in version 0.99.5 (2016-09-15) o add arguments colour and transparency for functions plotCircos and highlight Changes in version 0.99.4 (2016-08-17) o add arguments splitIndMZ and splitIndRT in function convert2MSP and fix bug (colnames classes instead of class) in convert2MSP o update vignette, unit tests and manuals [2016-08-17 Wed] Changes in version 0.99.3 (2016-08-01) o remove verbatim Textouput(help) in shinyApp o change function createSimilarityMatrix in order that it does not change ordering of row names o update unit tests and manuals Changes in version 0.99.2 (2016-07-26) o do not reorder again in createOrderedSimMat function o change allocatePrecursor2mz function such, that it is compatible with all sd01 and sd02 objects Changes in version 0.99.1 (2016-06-14) o rewrite functions that they do not require the argument dfNameGroup (data.frame containing group and unique identifier) any longer o the function binning uses now the function cut to create bins binning has two methods implemented to calculate from these bins median and mean m/z values from the fragment m/z values o documentation about data sets is extended o include 'Suggests: BiocGenerics' in the DESCRIPTION file Changes in version 0.99.0 (2016-05-14) o submit package to Bioconductor file tracker Changes in version 0.98.0 (2016-04-16) o add information of hovered objects in shinyCircos o allow for subsetting of MSP objects (2016-04-12) o add unit tests for exported functions (2016-04-12)