NEWS

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MetCirc 1.29.2 (2023-04-18)

• replace the error message in shinyCircos test

MetCirc 1.29.1 (2022-11-23)

• replace aes_string by aes since aes_string is deprecated in newest ggplot2 version

MetCirc 1.27.2 (2022-10-19)

• use Spectra from Spectra for spectral representation instead of MSpectra from MSnbase
• remove compare_Spectra and normalizeddotproduct functions and use compareSpectra from Spectra package
• change vignette from Rnw to Rmd

MetCirc 1.27.1 (2022-10-12)

• add ShinyApps in biocViews

MetCirc 1.19.0 (2020-07-02)

• adapt to changes in MSnbase (renaming of Spectra to MSpectra)

MetCirc 1.17.0 (2020-01-14)

• change unit tests to testthat
• change color 1:4 to colour character vector

MetCirc 1.15.2 (2019-09-09)

• add codecov
• add Travis-CI for continuous integration
• add CITATION file

MetCirc 1.15.1 (2019-08-29)

• add ggplot2 in dependencies
• change GPL-2 to GPL-3 license

MetCirc 1.15.0 (2019-04-23)

• implement the MSnbase Spectra/Spectrum2 as the container for MS2 spectra, change all functions that they accept Spectra objects
• write function convertMsp2Spectra that converts MSP files to Spectra files
• change data files: change convertMSP2MSP.RData to convertMsp2Spectra, create spectra.RData, update similarityMat.RData
• remove data files: binnedMSP.RData, idMSMStoMSP.RData

MetCirc 1.13.1 (2019-04-04)

• check if package passes R CMD build and R CMD check without any error messages and vignette can be run without any errors

MetCirc 1.11.1 (2018-10-22)

• 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

MetCirc 1.11.0 (2018-10-15)

• remove Makefile from directory vignettes/
• check if package passes R CMD build and R CMD check without any error messages and vignette can be run without any errors

MetCirc 1.9.0 (2018-04-16)

• 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

MetCirc 1.7.0 (2017-11-14)

• implement calculation for parameter m = 0 in NDP

MetCirc 1.5.0 (2017-10-20)

• 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

MetCirc 1.1.6 (2017-06-05)

• correct bug fix for msp binning when there is only one entry for msp entry
• improve function binning when there is only one fragment

MetCirc 1.1.5 (2017-04-03)

• extend unit tests for shinyApp, plottingFunctions and convert2MSP

MetCirc 1.1.4 (2017-01-28)

• change MSP class, create slots mz, rt, names, classes, information and adduct
• add tabPanels in shinyCircos (Main, Appearance)
• rearrange position of legend, implement option to show/not show legend
• rescale plot when changing window size, allow for further scaling/descaling of the plot
• adjust convertMSP2MSP to new class MSP, create unit tests
• include msp2msp matrix, a test data set for convertMSP2MSP
• set methods for names, classes, adduct and information
• change the interactive shinyCircos such that the user can update the annotation data of an MSP object (name, class, information and adduct ion information)

MetCirc 1.1.3 (2016-12-05)

• use new email adress
• use option to calculate MSP-object from msp-file directly

MetCirc 1.1.2 (2016-11-17)

• use absolute masses when calculating similarities in createSimilarityMatrix (bug fix)
• add option links in highlight, i.e. should links be plotted or not?

MetCirc 1.1.1 (2016-11-04)

• change slider input as such that one is able to select a lower and lower bound instead of only a lower bound

MetCirc 0.99.6 (2016-10-10)

• improve allocation of clicked features in shinyCircos
• change line width and colour in plotCircos

MetCirc 0.99.5 (2016-09-15)

• add arguments colour and transparency for functions plotCircos and highlight

MetCirc 0.99.4 (2016-08-17)

• add arguments splitIndMZ and splitIndRT in function convert2MSP and fix bug (colnames classes instead of class) in convert2MSP
• update vignette, unit tests and manuals [2016-08-17 Wed]

MetCirc 0.99.3 (2016-08-01)

• remove verbatim Textouput(help) in shinyApp
• change function createSimilarityMatrix in order that it does not change ordering of row names
• update unit tests and manuals

MetCirc 0.99.2 (2016-07-26)

• do not reorder again in createOrderedSimMat function
• change allocatePrecursor2mz function such, that it is compatible with all sd01 and sd02 objects

MetCirc 0.99.1 (2016-06-14)

• rewrite functions that they do not require the argument dfNameGroup (data.frame containing group and unique identifier) any longer
• 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
• documentation about data sets is extended
• include 'Suggests: BiocGenerics' in the DESCRIPTION file

MetCirc 0.99.0 (2016-05-14)

• submit package to Bioconductor file tracker

MetCirc 0.98.0 (2016-04-16)

• add information of hovered objects in shinyCircos
• allow for subsetting of MSP objects (2016-04-12)
• add unit tests for exported functions (2016-04-12)