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

In PlantDefenseMetabolism/MetabolomicTools: 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, msp = NULL, ...)

Arguments

similarityMatrix	matrix, similarityMatrix contains pair-wise similarity coefficients which give information about the similarity between MS/MS features
msp	MSP, an S4 object of class MSP, the MSP-object will be used to display information about the selected feature
...	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. When running shinyCircos with the object of class MSP, annotation data of selected MS/MS features will be displayed.

Value

shinyCircos returns a character vector with the (permanently) selected precursors or an object with the entries msp and selectedFeatures if a MSP-object was passed to shinyCircos

Author(s)

Thomas Naake, [e-mail]

Examples

data("idMSMStoMSP", package = "MetCirc")
## truncate files
finalMSP <- finalMSP[c(1:20, 29:48, 113:132, 240:259)]
data("binnedMSP", package = "MetCirc")
binnedMSP <- binnedMSP[c(1:20, 29:48, 113:132, 240:259),]
similarityMat <- createSimilarityMatrix(binnedMSP)
## Not run: shinyCircos(similarityMatrix = similarityMat, msp = finalMSP)

PlantDefenseMetabolism/MetabolomicTools documentation built on May 8, 2019, 2:53 p.m.