replayPlotAdd: Plot plotCircos or highlight

In MetCirc: Navigating mass spectral similarity in high-resolution MS/MS metabolomics data

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, [e-mail]

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)

MetCirc documentation built on Nov. 8, 2020, 8:26 p.m.