shinyCircos {MetCirc} | R Documentation

## Interactive visualisation of similarity and navigation of MS/MS features

### 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, thomasnaake@googlemail.com

### 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)

[Package MetCirc version 1.10.0 Index]