replayPlotAdd {MetCirc} | R Documentation

## Plot plotCircos or highlight

### Description

'replayPlotAdd' plots additional plots on a plot, either plots 'plotCircos' or 'highlight'.

### Usage

    replayPlotAdd(orderMatch = "mz", onCircle = FALSE, linkDf, mz_match,
      rt_match, clust_match, ind, indMz, indRT, indCluster)

### Arguments

`orderMatch` | orderMatch 'character', either '"mz"', '"retentionTime"' or '"clustering"'
`onCircle` | 'logical', are coordinates on circle. If FALSE and no features are selected ('length(ind) == 0'), then filled plots are replayed, otherwise highlighted plots are replayed.
`linkDf` | 'data.frame' that contains information of linked features for given thresholds
`mz_match` | 'character', ordered vector according to m/z
`rt_match` | 'character', ordered vector according to retention time
`clust_match` | 'character', ordered vector according to clustering
`ind` | 'numeric', indices of clicked features
`indMz` | 'numeric', indices of clicked features for '"mz"' ordering
`indRT` | 'numeric', indices of clicked features for '"retentionTime"' ordering
`indCluster` | 'numeric', indices of clicked features for '"clustering"' ordering

### Details

Helper function for 'shinyCircos'.

### Value

Depending on 'onCircle' and 'indMz' either returns 'plotCircos' or 'highlight'

### Author(s)

Thomas Naake, thomasnaake@googlemail.com

### Examples

    data("spectra", package="MetCirc")
    similarityMat <- compare_Spectra(spectra_tissue[1:10],
        fun=normalizeddotproduct, binSize=0.01)
    ## order according to retention time
    mz_match <- MetCirc:::typeMatch_link0(similarityMatrix=similarityMat, spectra=spectra_tissue,
        type="mz", condition=c("SPL", "LIM", "ANT", "STY"))
    linkDf <- mz_match[["link0df"]]
    mz_match <- mz_match[["type_match"]]
    rt_match <- MetCirc:::typeMatch_link0(similarityMatrix=similarityMat, spectra=spectra_tissue,
        type="retentionTime", condition=c("SPL", "LIM", "ANT", "STY"))
    rt_match <- rt_match[["type_match"]]
    clust_match <- MetCirc:::typeMatch_link0(similarityMatrix=similarityMat, spectra=spectra_tissue,
        type="clustering", condition=c("SPL", "LIM", "ANT", "STY"))
    clust_match <- clust_match[["type_match"]]
    circos.initialize(mz_match,##, levels = mz_match),
        xlim=matrix(rep(c(0,1), length(mz_match)), ncol=2, byrow=TRUE))
    #circos.trackPlotRegion(factor(mz_match, levels=mz_match), ylim=c(0,1))
    MetCirc:::replayPlotAdd(orderMatch="mz", onCircle=FALSE, linkDf=linkDf,
        mz_match=mz_match, rt_match=rt_match, clust_match=clust_match,
        ind=1, indMz=NULL, indRT=NULL, indCluster=NULL)

[Package MetCirc version 1.18.0 Index]