shinyCircos: Interactive visualisation of similarity and navigation of...

In MetCirc: Navigating mass spectral similarity in high-resolution MS/MS metabolomics data

Description

Visualise the similarity of MS/MS features in a reactive context. See 'Details' the vignette for further descriptions on how to use 'shinyCircos'.

Usage

shinyCircos(similarityMatrix, spectra, condition, ...)

Arguments

similarityMatrix	'matrix', 'similarityMatrix' contains pair-wise similarity coefficients which give information about the similarity between MS/MS features
spectra	an S4 object of class 'MSpectra', the 'MSpectra' object will be used to display information about the selected feature and will store information of annotation
condition	'character' vector, specifies which condtions/samples are displayed
...	further arguments passed to 'shinyCircos', e.g. 'cexFeatureNames' to pass to 'plotCircos' to set font size in 'plotCircos' of feature names

Details

The function is based on the 'shiny' and 'circlize' package. The user can choose interactively thresholds, type of links (between or within groups), display information about MS/MS features, permanently select MS/MS features and export selected precursors. The 'MSpectra' object stores annotation information about the MS/MS features. Names of features within the 'similarityMatrix' have to be found as entries in 'MSpectra'. 'names(MSpectra)' are used as identifiers and 'colnames'/'rownames' from 'similarityMatrix' are cleaved by the group identifier (separated by "_"). Annotation information is taken from 'spectra' from the columns "names", "information", "classes" and "adduct" in the slot 'elementMetadata' of 'spectra'. After exiting the application, the annotation will be written to the respective columns in the slot 'elementMetadata'. If one or several of these columns is already present in 'elementMetadata', the column(s) will be used as the source of annotation information.

Value

'character', 'shinyCircos' returns a 'character' vector with the permanently selected precursors and an object with the 'MSpectra' object containing the annotation.

Author(s)

Thomas Naake, [e-mail]

Examples

data("spectra", package = "MetCirc")
similarityMat <- compare_Spectra(spectra_tissue[1:10],
    fun = normalizeddotproduct, binSize = 0.01)
## Not run: 
shinyCircos(similarityMatrix = similarityMat, 
    spectra = spectra_tissue, condition = c("SPL", "LIM", "ANT", "STY"))

## End(Not run)

MetCirc documentation built on Nov. 8, 2020, 8:26 p.m.