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 1.17.0 Index]