# Navigating mass spectral similarity in high-resolution MS/MS metabolomics data

## Documentation for package ‘MetCirc’ version 1.20.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

cart2Polar | Calculate polar coordinates from cartesian coordinates
circosLegend | Plot a legend for circos plot
compare_Spectra | Create similarity matrix from 'MSnbase::MSpectra' object
compartmentTissue | Example data for 'MetCirc': 'compartmentTissue'
convertExampleDF | Example data for 'MetCirc': convertExampleDF
convertMsp2Spectra | Convert MSP data frame into object of class 'MSpectra'
createLink0df | Create a link matrix
createLinkDf | Create a data frame which contains features to link (indices)
cutLinkDf | Create a cut data frame with information on links
getLinkDfIndices | Get indices in linkDf of feature
highlight | Add links and highlight sectors
minFragCart2Polar | Calculate the nearest feature in polar coordinates given cartesian coordinates
msp2spectra | Example data for 'MetCirc': 'msp2spectra'
neutralloss | Calculate similarity based on neutral losses
normalizeddotproduct | Calculate the normalized dot product
orderSimilarityMatrix | Order columns and rows of a similarity matrix according to m/z, retention time and clustering
plotCircos | Circular plot to visualise similarity
plotSpectra | Plot pair-wise spectra
printInformationSelect | Display information on connected features of selected features
recordPlotFill_degreeFeatures | Record a plot of filled features and the degree of features
recordPlotHighlight | Return a 'recordedplot' of 'plotCircos' plot with 'highlight = TRUE'
replayPlotAdd | Plot plotCircos or highlight
replayPlotOrder | Wrapper for 'replayPlot'
sd01_outputXCMS | Example data for 'MetCirc': 'sd01_outputXCMS'
sd02_deconvoluted | Example data for 'MetCirc': sd02_deconvoluted
select | Select variable based on condition
shinyCircos | Interactive visualisation of similarity and navigation of MS/MS features
similarityMat | Example data for 'MetCirc': 'similarityMat'
spectraCond | Get MS/MS spectra that are present in condition
spectra_tissue | Example data for 'MetCirc': 'spectra_tissue'
thresholdLinkDf | Threshold a data frame containing information on links
tissue | Example data for 'MetCirc': 'tissue'
typeMatch_link0 | Get typeMatch and link0 data frame