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PeakML.Isotope.processUntargettedIsotopes <- function(peakMLFile, analyse, databases, outDirectory, outFileName, layoutMtx, ppm, stdRTWindow, sampleNames, peakDataMtx, chromDataList, phenoData, sampleGroups, plotOrder, mzXMLSrc, fillGaps, massCorrection, useArea, filterStringency, baseCorrection, numSlaves, label, exclude_from_plots) {
molFrames <- list()
if (analyse == "databases"){
mFrame <- PeakML.Isotope.ReadDB(databases)
if (!numSlaves==1){
# Split the matrix into small chunks and save as a list of dataframes
startPoints <- seq(1, length(row.names(mFrame)), round(length(row.names(mFrame))/numSlaves))
for (sp in 1:length(startPoints)){
start <- startPoints[sp]
if (!is.na(startPoints[sp+1])){
end <- startPoints[sp+1]-1
} else {
end <- length(row.names(mFrame))
}
dFrame <- mFrame[start:end,]
dFrame$rt <-NA
dFrame$follow <- NA
molFrames [[sp]] <- dFrame
}
} else {
dFrame <- mFrame
dFrame$rt <- NA
dFrame$follow <- NA
molFrames [[1]] <- dFrame
}
}
if (analyse == "identified"){
mFrame <- PeakML.Isotope.DB2Text(peakMLFile, databases)
if (!numSlaves ==1 ){
startPoints <- seq(1, length(row.names(mFrame)), round(length(row.names(mFrame))/numSlaves))
for (sp in 1:length(startPoints)){
start <- startPoints[sp]
if (!is.na(startPoints[sp+1])){
end <- startPoints[sp+1]-1
} else {
end <- length(row.names(mFrame))
}
dFrame <- mFrame[start:end,]
dFrame$rt <- NA
dFrame$follow <- NA
molFrames [[sp]] <- dFrame
}
} else {
molFrames[[1]] <- mFrame
}
}
if (!numSlaves == 1){
plotUtgt <- function(index){
require(mzmatch.R)
mzmatch.init()
PeakML.Isotope.plotUntargettedIsotopes (peakMLFile, molFrames[[index]], outDirectory, paste(outFileName, index, sep="_"), layoutMtx, ppm, stdRTWindow, sampleNames, peakDataMtx, chromDataList, phenoData, sampleGroups, plotOrder, mzXMLSrc, fillGaps, massCorrection, useArea, filterStringency, baseCorrection, label, exclude_from_plots)
}
cl <- makeCluster (numSlaves)
assign ("peakMLFile", peakMLFile, envir=.GlobalEnv)
assign ("molFrames", molFrames, envir=.GlobalEnv)
assign ("outDirectory", outDirectory, envir=.GlobalEnv)
assign ("outFileName", outFileName, envir=.GlobalEnv)
assign ("layoutMtx", layoutMtx, envir=.GlobalEnv)
assign ("ppm", ppm, envir=.GlobalEnv)
assign ("stdRTWindow", stdRTWindow, envir=.GlobalEnv)
assign ("sampleNames",sampleNames, envir=.GlobalEnv)
assign ("peakDataMtx", peakDataMtx, envir=.GlobalEnv)
assign ("chromDataList", chromDataList, envir=.GlobalEnv)
assign ("phenoData", phenoData, envir=.GlobalEnv)
assign ("sampleGroups", sampleGroups, envir=.GlobalEnv)
assign ("plotOrder",plotOrder, envir=.GlobalEnv)
assign ("mzXMLSrc", mzXMLSrc, envir=.GlobalEnv)
assign ("fillGaps",fillGaps, envir=.GlobalEnv)
assign ("massCorrection",massCorrection , envir=.GlobalEnv)
assign ("useArea",useArea, envir=.GlobalEnv)
assign ("filterStringency",filterStringency, envir=.GlobalEnv)
assign ("baseCorrection",baseCorrection, envir=.GlobalEnv)
assign ("label",label, envir=.GlobalEnv)
assign ("exclude_from_plots", label, envir=.GlobalEnv)
vars <- list("peakMLFile", "molFrames", "outDirectory", "outFileName", "layoutMtx", "ppm", "stdRTWindow", "sampleNames", "peakDataMtx", "chromDataList", "phenoData", "sampleGroups", "plotOrder", "mzXMLSrc", "fillGaps", "massCorrection", "useArea", "filterStringency", "baseCorrection", "label", "exclude_from_plots")
clusterExport (cl, list=vars)
system.time(clusterApply(cl, 1:length(molFrames), plotUtgt))
stopCluster(cl)
} else {
PeakML.Isotope.plotUntargettedIsotopes (peakMLFile, molFrames[[1]], outDirectory, outFileName, layoutMtx, ppm, stdRTWindow, sampleNames, peakDataMtx, chromDataList, phenoData, sampleGroups, plotOrder, mzXMLSrc, fillGaps, massCorrection, useArea, filterStringency, baseCorrection, label, exclude_from_plots)
}
}
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