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 1.20.0 Index]