Nothing
R/CompareComplexStdFromTable.R
In mqqc: Quality control of LCMS derived proteomic data
Defines functions
CompareComplexStdFromTable
CompareComplexStdFromTable <-
function(tempListOne, RESettings, pdfShow = F, finalMQQC , PDFname = "ComplexStdComparison.pdf",main = NULL, logPlot = "n", TargetVec = "ECstd",PDF = T,Machines = NULL,StandardIDs = c("ECstd","BSA")){
#TargetVec <- StandardIDs[1]
#uniSample <- tempListOne#[grep(TargetVec, tempListOne$Name),]
test <- sub(RESettings$REmac,"", as.character(tempListOne$Name))
UniMachine <- grepRE(as.character(tempListOne$Name),RESettings$REmac)
if(length(Machines) > 0){
# test <<- test
MachineVec <- grep(paste(Machines,collapse = "|"), UniMachine)
if(length(MachineVec) > 0){
tempListOne <- tempListOne[MachineVec,]
UniMachine <- UniMachine[MachineVec]
}
}
pdfName <- paste(finalMQQC ,"TimeLines", PDFname,sep = "/")
if(PDF){
pdf(pdfName ,width = 14,height = 11,pointsize = 15)
}else{
scaleFactor <- 1.7
jpeg(pdfName,width = 140*15/scaleFactor,height = 120*15/scaleFactor, quality = 90,pointsize = 10/(scaleFactor))
}
M <- matrix(c(1,1,1,2,3,4,5,6,7,8,9,10),4,3,byrow = T)
M <- cbind(M,rep(max(M)+1,dim(M)[1]))
layout(M,height = c(0.1,1,1),width = c(1,1,1,0.4))
par(mai = rep(0,4),lwd = 2)
empty.plot()
if(length(main ) == 0){
main <- paste("MQQC Parameter Comparisons, Complex Standard (",TargetVec,") ",Sys.Date(),sep = "")
}
if(PDF){
mtext(main,line = -2,cex = 1.52)
par(mai = c(0.5,0.5,0.2,0.1))
lwdjpg <- 1
}else{
mtext(main,line = -7,cex = 5)
par(mai = c(0.7,0.7,0.2,0.1),lwd = 3,cex =3)
lwdjpg <- 2/scaleFactor
}
# Score Dependecne
#PlotTwoFun(tempListOne = tempListOne,"Intensity.50.","score.50.","MS Intensity","MQ Score")
# tempListOne <<- tempListOne
if(TargetVec == StandardIDs[2]&TargetVec!= ""){
try(PlotTwoFun(tempListOne = tempListOne,"MSID.min","Coverage","Isotopic Patterns [1/min]","Coverage [%]", logPlot = "",leg = F,shiftPlot = T,UniMachine = UniMachine, Machines = Machines,lwdjpg = lwdjpg,PDF =PDF),silent = T)
try(PlotTwoFun(tempListOne = tempListOne,"Intensity.50.","Coverage","MS Median Intensity","Coverage [%]", logPlot = "",leg = F,shiftPlot = T,UniMachine = UniMachine, Machines = Machines,lwdjpg = lwdjpg,PDF =PDF),silent = T)
try(PlotTwoFun(tempListOne = tempListOne,"precision.50.","Coverage","MS Mass Precision [ppm]","Coverage [%]",logPlot = "",leg = F,shiftPlot = T,UniMachine = UniMachine, Machines = Machines,lwdjpg = lwdjpg,PDF =PDF),silent = T)
try(PlotTwoFun(tempListOne = tempListOne,"msmsQuantile.50.","Coverage","MSMS Median Fragment Counts","Coverage [%]",leg = F,shiftPlot = T,UniMachine = UniMachine, Machines = Machines,lwdjpg = lwdjpg,PDF =PDF),silent = T)
try(PlotTwoFun(tempListOne = tempListOne,"msmsMassCount.50.","Coverage","MSMS/min","Coverage [%]",leg = F,shiftPlot = T,UniMachine = UniMachine, Machines = Machines,lwdjpg = lwdjpg,PDF =PDF),silent = T)
try(PlotTwoFun(tempListOne = tempListOne,"LCcombiScore","Coverage","LC Score","Coverage [%]",leg = F,shiftPlot = T,UniMachine = UniMachine, Machines = Machines,lwdjpg = lwdjpg,PDF =PDF),silent = T)
try(PlotTwoFun(tempListOne = tempListOne,"ret.width.50.","Coverage","LC Peak Width","Coverage [%]",leg = F,shiftPlot = T,UniMachine = UniMachine, Machines = Machines,lwdjpg = lwdjpg,PDF =PDF),silent = T)
try(LegFun <- PlotTwoFun(tempListOne = tempListOne,"ret.peak.shape.abs.50.","Coverage","LC Peak Symmetry","Coverage [%]", logPlot = "",leg = F,shiftPlot = T,UniMachine = UniMachine, Machines = Machines,lwdjpg = lwdjpg,PDF =PDF),silent = T)
try(empty.plot())
}else{
# MSID.min
try(PlotTwoFun(tempListOne = tempListOne,"MSID.min","quan.msms.min","MS Isotopic Patterns [1/min]","PSMs [1/min]", logPlot = "",leg = F,shiftPlot = T,UniMachine = UniMachine, Machines = Machines,lwdjpg = lwdjpg,PDF =PDF),silent = F)
try(PlotTwoFun(tempListOne = tempListOne,"Intensity.50.","quan.msms.min","MS Median Intensity","PSMs [1/min]", logPlot = "",leg = F,shiftPlot = T,UniMachine = UniMachine, Machines = Machines,lwdjpg = lwdjpg,PDF =PDF),silent = T)
try(PlotTwoFun(tempListOne = tempListOne,"precision.50.","quan.msms.min","MS Mass Precision","PSMs [1/min]",logPlot = "",leg = F,shiftPlot = T,UniMachine = UniMachine, Machines = Machines,lwdjpg = lwdjpg,PDF =PDF),silent = T)
try(PlotTwoFun(tempListOne = tempListOne,"msmsQuantile.50.","quan.msms.min","MSMS Median Fragment Intensity","PSMs [1/min]",logPlot = "",leg = F,shiftPlot = T,UniMachine = UniMachine, Machines = Machines,lwdjpg = lwdjpg,PDF =PDF),silent = T)
try(PlotTwoFun(tempListOne = tempListOne,"msmsMassCount.50.","quan.msms.min","MSMS Median Fragment Counts","PSMs [1/min]",logPlot = "",leg = F,shiftPlot = T,UniMachine = UniMachine, Machines = Machines,lwdjpg = lwdjpg,PDF =PDF),silent = T)
try(PlotTwoFun(tempListOne = tempListOne,"LCcombiScore","quan.msms.min","LC Score","PSMs [1/min]",logPlot = "",leg = F,shiftPlot = T,UniMachine = UniMachine, Machines = Machines,lwdjpg = lwdjpg,PDF =PDF),silent = T)
try(PlotTwoFun(tempListOne = tempListOne,"ret.width.50.","quan.msms.min","LC Peak Width","PSMs [1/min]",logPlot = "",leg = F,shiftPlot = T,UniMachine = UniMachine, Machines = Machines,lwdjpg = lwdjpg,PDF =PDF),silent = T)
try(LegFun <- PlotTwoFun(tempListOne = tempListOne,"ret.peak.shape.abs.50.","quan.msms.min","LC Peak Symmetry","PSMs [1/min]", logPlot = "",leg = F,shiftPlot = T,UniMachine = UniMachine, Machines = Machines,lwdjpg = lwdjpg,PDF =PDF),silent = F)
try(empty.plot())
}
if(exists("LegFun")){
par(mai = rep(0,4),mar = rep(0,4))
empty.plot()
legend("left"
,legend = as.character(LegFun$Mac)
,col = as.character(LegFun$col)
,lwd = LegFun$lwd,
,lty = LegFun$lty
,pch = LegFun$pch,
,border = "transparent",box.col = "transparent",bg = "#FFFFFF80",xpd = NA
)
}
graphics.off()
if(pdfShow){
try(system(paste("open", pdfName)))
}
DensMatrixTemplate <- rbind(
#MS
c("Isotope.patterns.min","Features/min",F,"MS"),
c("Intensity.50.","log10 MS Median Intensity",T,"MS"),
c("precision.50.","Mass precision [ppm]",F,"MS"),
c("Coverage","Coverage",F,"MS"),
#MSMS
c("quan.msms.min","IDs/min",F,"MSMS"),
c("msmsQuantile.50.","log10 MSMS Median Intensity",T,"MSMS"),
c("msmsMassCount.50.","MSMS Median Fragment Counts",F,"MSMS"),
#nlc
c("LCcombiScore","LC profile distribution",F,"LC"),
c("ret.width.50.","Retention Time [min]",F,"LC"),
c("ret.peak.shape.abs.50.","log10 Peak symmetry",T,"LC"))
if(TargetVec == StandardIDs[2]&TargetVec!= ""){
}else{
DensMatrixTemplate <- DensMatrixTemplate[grep("Coverage",DensMatrixTemplate[,1],invert = T),]
}
graphics.off()
pdfName <- paste(finalMQQC ,"TimeLines", paste("DensityEstimates",PDFname,sep = "_"),sep = "/")
if(PDF){
pdf(pdfName ,width = 12,height = 0.5*dim(DensMatrixTemplate)[1])
par(mai = c(0.3,0.5,0.2,0.2),las = 1)
}else{
scaleFactor <- 1.2
jpeg(pdfName,width = 1000,height = 50*dim(DensMatrixTemplate)[1], quality = 90,pointsize = 12)
par(mai = c(0.3,0.5,0.2,0.2),las = 1)
}
#pdf(pdfname<- "MQQCDensityPlots.pdf",)
vmax <- max(table(DensMatrixTemplate[,4]))
colmax <- length(unique(DensMatrixTemplate[,4]))
LayoutM <- matrix(1:(vmax*colmax),vmax,colmax)
LayoutM <- cbind(LayoutM,LegPlot<- max(LayoutM)+1)
layout(LayoutM,width = c(rep(1,colmax),0.8))
LegFun <- LegFun
PointsListQuantiles <- list()
itMain = 0
naQuan <- c()
try(rm(tempI),silent = T)
for(i in unique(DensMatrixTemplate[,4])){
cat("\r Preparing Comparison Plots",i)
tempDensMatrix <- DensMatrixTemplate[DensMatrixTemplate[,4]== i,]
for(a in 1:vmax){
itMain = itMain +1
if(a > dim(tempDensMatrix)[1]){
empty.plot()
}else{
tempI <- tempListOne[,tolower(colnames(tempListOne)) == tolower(tempDensMatrix[a,1])]
# if(all(is.na(Current))){
# }
tempDensMatrix <- tempDensMatrix
if(length(tempI) > 0){
if(tempDensMatrix[a,3] == "TRUE"){
tempI <- log10(tempI)
}
CurrentL <- lapply(unique(UniMachine),function(x){
sel <- x == UniMachine
tempM <- tempListOne[sel,]
na <- tempListOne$Name[sel][tempM$System.Time.s == max(tempM$System.Time.s,na.rm = T)]
Current <- tempI[sel][tempM$System.Time.s == max(tempM$System.Time.s,na.rm = T)]
return(c(Current,na))
})
names(CurrentL) <- unique(UniMachine)
tempM <- aggregate(tempI,list(UniMachine),median,na.rm = T)
temp <- aggregate(tempI,list(UniMachine),function(x){
# x <<- x
tempDens <- list(x = 0,y = 0)
tempi <- class(try(tempDens <- density(x,na.rm = T),silent = T))
tempDens$Quantile <- quantile(x,prob = c(0.75,0.95,0.5,0.25,0.05),na.rm = T)
if(tempi!="try-error"){
tempDens$y <- tempDens$y /max(tempDens$y,na.rm = T)
}
return(tempDens)}
)
OrderFun <- merge.control(temp$Group.1,LegFun$Mac)
xlim <- range(tempI[!is.infinite(tempI)],na.rm = T)
if(!any(c(is.na(xlim),is.infinite(xlim)))){
plot(1,type = "n",ylim = c(0,1),xlim =xlim ,xlab = "",main = tempDensMatrix[a,2],ylab = "",frame = F)
}else{
plot(1,type = "n",ylim = c(0,1) ,xlab = "",main = tempDensMatrix[a,2],ylab = "",frame = F)
}
itCompare <<- 0
# pointsList <<- list()
pointsList <- sapply(OrderFun,function(x){
itCompare <<- itCompare+1
if(is.matrix(temp$x)){
subDens <- temp$x[x,]
}else{
subDens <- temp$x[[x]]
}
if(exists("subDens")){
try(subDens$y <- subDens$y /max(subDens$y ))
trye <- class(try(points(subDens,col = LegFun$col[itCompare],lty = 1,type = "l",lwd = LegFun$lwd),silent = T))
Current <- CurrentL[[itCompare]]
CurrentDiff <- abs(subDens$x-as.numeric(Current[1]))
Currenty <- subDens$y[CurrentDiff == min(CurrentDiff,na.rm = T)]
Currenty <- Currenty[!is.na(Currenty)]
if(length(Currenty)==0){Currenty <- NA}
pointsList<- c(as.numeric(Current[1]),Currenty,col = LegFun$col[itCompare],pch = LegFun$pch[itCompare],subDens$Quantile)
# try(points())
if(trye!="try-error"){
try(xl<- median(tempM[x,2],na.rm = T),silent = T)
#abline(v = xl<- median(tempM[x,2],na.rm = T),col = LegFun$col[x],lty = "dotted")
try(subvec <- abs(xl -subDens$x) ,silent = T)
try(yl <- subDens$y[subvec == min(subvec,na.rm = T)][1],silent = T)
try(lines(c(xl,xl),c(0,yl),col = LegFun$col[itCompare],lty = "dotted"),silent =T)
try(axis(1,at = xl,col = LegFun$col[itCompare],label = ""),silent = T)
}
}else{ pointsList<- c(Current,rep(NA,9))
}
return(pointsList)
})
# pointsList <<-pointsList
apply(pointsList,2,function(x){
try(points(x[1],x[2],bg = "white",col = "white",pch = 23,cex = 1.85,lwd = 0.5),silent = T)
return(NULL)
})
apply(pointsList,2,function(x){
try(points(x[1],x[2],col = x[3],pch = as.numeric(x[4]),cex = 1,xpd = NA),silent = F)
return(NULL)
})
pointsList <- pointsList[grep("%",rownames(pointsList)),]
try(colnames(pointsList) <- LegFun$Mac,silent = T) # check if naming is correct
PointsListQuantiles[[itMain]] <- pointsList
}else{
plot(1,type = "n",ylim = c(0,1),xlab = "",main = tempDensMatrix[a,2],ylab = "",frame = F)
}
}
}
naQuan <- c(naQuan,tempDensMatrix[,1])
}
names(PointsListQuantiles)<- naQuan
par(mai = rep(0,4),mar = rep(0,4))
empty.plot()
# CurrentL <<- CurrentL
CL <- sapply(CurrentL,function(x){x[2]})
names(CL) <- names(CurrentL)
CL <- CL[match(names(CL),as.character(LegFun$Mac))]
# LegFun <<- LegFun
legend("left"
,legend = paste(as.character(LegFun$Mac),CL,sep = "\n")
,col = as.character(LegFun$col)
,lwd = LegFun$lwd,
,border = "transparent",box.col = "transparent",bg = "#FFFFFF80",xpd = NA,y.intersp = 2
)
legend("topright",legend = Sys.Date(),bty = "n")
graphics.off()
if(pdfShow){
try(system(paste("open",pdfName)))
}
# system(paste("open",pdfName))
# LoadSettings(inputframe = tempListOne,DensMatrixTemplate = DensMatrixTemplate,pdfname = paste(finalMQQC ,"TimeLines", paste("Correlations",PDFname,sep = "_"),sep = "/"),pdfshow = F)
cat("\rPreparing Timelines")
try(PairsFun(inputframe = tempListOne,DensMatrixTemplate = DensMatrixTemplate,pdfname = paste(finalMQQC ,"TimeLines", paste("Correlations",PDFname,sep = "_"),sep = "/"),pdfshow = F),silent = T)
return(PointsListQuantiles)
}
# try(trash <-CompareComplexStdFromTable(collectList[ECstd,],RESettings,F,finalMQQC, PDFname = "ComplexStandardComparison.jpg", TargetVec = StandardIDs[1],PDF = F, Machines = Machines),silent = T)
# try(RestQuan <- CompareComplexStdFromTable(collectList[Normal,],RESettings,F,finalMQQC, PDFname = "NormalSampleComparison.pdf",main = "MQQC Normal Samples Parameter Comparison", TargetVec = "",PDF = T, Machines = Machines,pdfShow = T),silent = F)
# try(trash <-CompareComplexStdFromTable(tempListOne = collectList[ECstd,],RESettings = RESettings,pdfShow = T,finalMQQC = finalMQQC, PDFname = "ComplexStandardComparison.pdf", TargetVec = StandardIDs[1],PDF = T, Machines = Machines),silent = F)
# try(ECquan <- CompareComplexStdFromTable(tempListOne = collectList[ECstd,],RESettings = RESettings,finalMQQC = finalMQQC, PDFname = "ComplexStandardComparison.jpg", TargetVec = StandardIDs[1],PDF = F, Machines = unique(strsplitslot(unique(tempListOne$Name),1,"_",fixed = T)),StandardIDs = StandardIDs,pdfShow = T),silent = F)
# try(ECquan <- CompareComplexStdFromTable(tempListOne = collectList[ECstd,],pdfShow = T,RESettings = RESettings,finalMQQC = finalMQQC, PDFname = "ComplexStandardComparison.pdf", TargetVec = StandardIDs[1],PDF = T, Machines = Machines,StandardIDs = StandardIDs),silent = T)
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Defines functions CompareComplexStdFromTable
CompareComplexStdFromTable <-
function(tempListOne, RESettings, pdfShow = F, finalMQQC , PDFname = "ComplexStdComparison.pdf",main = NULL, logPlot = "n", TargetVec = "ECstd",PDF = T,Machines = NULL,StandardIDs = c("ECstd","BSA")){
#TargetVec <- StandardIDs[1]
#uniSample <- tempListOne#[grep(TargetVec, tempListOne$Name),]
test <- sub(RESettings$REmac,"", as.character(tempListOne$Name))
UniMachine <- grepRE(as.character(tempListOne$Name),RESettings$REmac)
if(length(Machines) > 0){
# test <<- test
MachineVec <- grep(paste(Machines,collapse = "|"), UniMachine)
if(length(MachineVec) > 0){
tempListOne <- tempListOne[MachineVec,]
UniMachine <- UniMachine[MachineVec]
}
}
pdfName <- paste(finalMQQC ,"TimeLines", PDFname,sep = "/")
if(PDF){
pdf(pdfName ,width = 14,height = 11,pointsize = 15)
}else{
scaleFactor <- 1.7
jpeg(pdfName,width = 140*15/scaleFactor,height = 120*15/scaleFactor, quality = 90,pointsize = 10/(scaleFactor))
}
M <- matrix(c(1,1,1,2,3,4,5,6,7,8,9,10),4,3,byrow = T)
M <- cbind(M,rep(max(M)+1,dim(M)[1]))
layout(M,height = c(0.1,1,1),width = c(1,1,1,0.4))
par(mai = rep(0,4),lwd = 2)
empty.plot()
if(length(main ) == 0){
main <- paste("MQQC Parameter Comparisons, Complex Standard (",TargetVec,") ",Sys.Date(),sep = "")
}
if(PDF){
mtext(main,line = -2,cex = 1.52)
par(mai = c(0.5,0.5,0.2,0.1))
lwdjpg <- 1
}else{
mtext(main,line = -7,cex = 5)
par(mai = c(0.7,0.7,0.2,0.1),lwd = 3,cex =3)
lwdjpg <- 2/scaleFactor
}
# Score Dependecne
#PlotTwoFun(tempListOne = tempListOne,"Intensity.50.","score.50.","MS Intensity","MQ Score")
# tempListOne <<- tempListOne
if(TargetVec == StandardIDs[2]&TargetVec!= ""){
try(PlotTwoFun(tempListOne = tempListOne,"MSID.min","Coverage","Isotopic Patterns [1/min]","Coverage [%]", logPlot = "",leg = F,shiftPlot = T,UniMachine = UniMachine, Machines = Machines,lwdjpg = lwdjpg,PDF =PDF),silent = T)
try(PlotTwoFun(tempListOne = tempListOne,"Intensity.50.","Coverage","MS Median Intensity","Coverage [%]", logPlot = "",leg = F,shiftPlot = T,UniMachine = UniMachine, Machines = Machines,lwdjpg = lwdjpg,PDF =PDF),silent = T)
try(PlotTwoFun(tempListOne = tempListOne,"precision.50.","Coverage","MS Mass Precision [ppm]","Coverage [%]",logPlot = "",leg = F,shiftPlot = T,UniMachine = UniMachine, Machines = Machines,lwdjpg = lwdjpg,PDF =PDF),silent = T)
try(PlotTwoFun(tempListOne = tempListOne,"msmsQuantile.50.","Coverage","MSMS Median Fragment Counts","Coverage [%]",leg = F,shiftPlot = T,UniMachine = UniMachine, Machines = Machines,lwdjpg = lwdjpg,PDF =PDF),silent = T)
try(PlotTwoFun(tempListOne = tempListOne,"msmsMassCount.50.","Coverage","MSMS/min","Coverage [%]",leg = F,shiftPlot = T,UniMachine = UniMachine, Machines = Machines,lwdjpg = lwdjpg,PDF =PDF),silent = T)
try(PlotTwoFun(tempListOne = tempListOne,"LCcombiScore","Coverage","LC Score","Coverage [%]",leg = F,shiftPlot = T,UniMachine = UniMachine, Machines = Machines,lwdjpg = lwdjpg,PDF =PDF),silent = T)
try(PlotTwoFun(tempListOne = tempListOne,"ret.width.50.","Coverage","LC Peak Width","Coverage [%]",leg = F,shiftPlot = T,UniMachine = UniMachine, Machines = Machines,lwdjpg = lwdjpg,PDF =PDF),silent = T)
try(LegFun <- PlotTwoFun(tempListOne = tempListOne,"ret.peak.shape.abs.50.","Coverage","LC Peak Symmetry","Coverage [%]", logPlot = "",leg = F,shiftPlot = T,UniMachine = UniMachine, Machines = Machines,lwdjpg = lwdjpg,PDF =PDF),silent = T)
try(empty.plot())
}else{
# MSID.min
try(PlotTwoFun(tempListOne = tempListOne,"MSID.min","quan.msms.min","MS Isotopic Patterns [1/min]","PSMs [1/min]", logPlot = "",leg = F,shiftPlot = T,UniMachine = UniMachine, Machines = Machines,lwdjpg = lwdjpg,PDF =PDF),silent = F)
try(PlotTwoFun(tempListOne = tempListOne,"Intensity.50.","quan.msms.min","MS Median Intensity","PSMs [1/min]", logPlot = "",leg = F,shiftPlot = T,UniMachine = UniMachine, Machines = Machines,lwdjpg = lwdjpg,PDF =PDF),silent = T)
try(PlotTwoFun(tempListOne = tempListOne,"precision.50.","quan.msms.min","MS Mass Precision","PSMs [1/min]",logPlot = "",leg = F,shiftPlot = T,UniMachine = UniMachine, Machines = Machines,lwdjpg = lwdjpg,PDF =PDF),silent = T)
try(PlotTwoFun(tempListOne = tempListOne,"msmsQuantile.50.","quan.msms.min","MSMS Median Fragment Intensity","PSMs [1/min]",logPlot = "",leg = F,shiftPlot = T,UniMachine = UniMachine, Machines = Machines,lwdjpg = lwdjpg,PDF =PDF),silent = T)
try(PlotTwoFun(tempListOne = tempListOne,"msmsMassCount.50.","quan.msms.min","MSMS Median Fragment Counts","PSMs [1/min]",logPlot = "",leg = F,shiftPlot = T,UniMachine = UniMachine, Machines = Machines,lwdjpg = lwdjpg,PDF =PDF),silent = T)
try(PlotTwoFun(tempListOne = tempListOne,"LCcombiScore","quan.msms.min","LC Score","PSMs [1/min]",logPlot = "",leg = F,shiftPlot = T,UniMachine = UniMachine, Machines = Machines,lwdjpg = lwdjpg,PDF =PDF),silent = T)
try(PlotTwoFun(tempListOne = tempListOne,"ret.width.50.","quan.msms.min","LC Peak Width","PSMs [1/min]",logPlot = "",leg = F,shiftPlot = T,UniMachine = UniMachine, Machines = Machines,lwdjpg = lwdjpg,PDF =PDF),silent = T)
try(LegFun <- PlotTwoFun(tempListOne = tempListOne,"ret.peak.shape.abs.50.","quan.msms.min","LC Peak Symmetry","PSMs [1/min]", logPlot = "",leg = F,shiftPlot = T,UniMachine = UniMachine, Machines = Machines,lwdjpg = lwdjpg,PDF =PDF),silent = F)
try(empty.plot())
}
if(exists("LegFun")){
par(mai = rep(0,4),mar = rep(0,4))
empty.plot()
legend("left"
,legend = as.character(LegFun$Mac)
,col = as.character(LegFun$col)
,lwd = LegFun$lwd,
,lty = LegFun$lty
,pch = LegFun$pch,
,border = "transparent",box.col = "transparent",bg = "#FFFFFF80",xpd = NA
)
}
graphics.off()
if(pdfShow){
try(system(paste("open", pdfName)))
}
DensMatrixTemplate <- rbind(
#MS
c("Isotope.patterns.min","Features/min",F,"MS"),
c("Intensity.50.","log10 MS Median Intensity",T,"MS"),
c("precision.50.","Mass precision [ppm]",F,"MS"),
c("Coverage","Coverage",F,"MS"),
#MSMS
c("quan.msms.min","IDs/min",F,"MSMS"),
c("msmsQuantile.50.","log10 MSMS Median Intensity",T,"MSMS"),
c("msmsMassCount.50.","MSMS Median Fragment Counts",F,"MSMS"),
#nlc
c("LCcombiScore","LC profile distribution",F,"LC"),
c("ret.width.50.","Retention Time [min]",F,"LC"),
c("ret.peak.shape.abs.50.","log10 Peak symmetry",T,"LC"))
if(TargetVec == StandardIDs[2]&TargetVec!= ""){
}else{
DensMatrixTemplate <- DensMatrixTemplate[grep("Coverage",DensMatrixTemplate[,1],invert = T),]
}
graphics.off()
pdfName <- paste(finalMQQC ,"TimeLines", paste("DensityEstimates",PDFname,sep = "_"),sep = "/")
if(PDF){
pdf(pdfName ,width = 12,height = 0.5*dim(DensMatrixTemplate)[1])
par(mai = c(0.3,0.5,0.2,0.2),las = 1)
}else{
scaleFactor <- 1.2
jpeg(pdfName,width = 1000,height = 50*dim(DensMatrixTemplate)[1], quality = 90,pointsize = 12)
par(mai = c(0.3,0.5,0.2,0.2),las = 1)
}
#pdf(pdfname<- "MQQCDensityPlots.pdf",)
vmax <- max(table(DensMatrixTemplate[,4]))
colmax <- length(unique(DensMatrixTemplate[,4]))
LayoutM <- matrix(1:(vmax*colmax),vmax,colmax)
LayoutM <- cbind(LayoutM,LegPlot<- max(LayoutM)+1)
layout(LayoutM,width = c(rep(1,colmax),0.8))
LegFun <- LegFun
PointsListQuantiles <- list()
itMain = 0
naQuan <- c()
try(rm(tempI),silent = T)
for(i in unique(DensMatrixTemplate[,4])){
cat("\r Preparing Comparison Plots",i)
tempDensMatrix <- DensMatrixTemplate[DensMatrixTemplate[,4]== i,]
for(a in 1:vmax){
itMain = itMain +1
if(a > dim(tempDensMatrix)[1]){
empty.plot()
}else{
tempI <- tempListOne[,tolower(colnames(tempListOne)) == tolower(tempDensMatrix[a,1])]
# if(all(is.na(Current))){
# }
tempDensMatrix <- tempDensMatrix
if(length(tempI) > 0){
if(tempDensMatrix[a,3] == "TRUE"){
tempI <- log10(tempI)
}
CurrentL <- lapply(unique(UniMachine),function(x){
sel <- x == UniMachine
tempM <- tempListOne[sel,]
na <- tempListOne$Name[sel][tempM$System.Time.s == max(tempM$System.Time.s,na.rm = T)]
Current <- tempI[sel][tempM$System.Time.s == max(tempM$System.Time.s,na.rm = T)]
return(c(Current,na))
})
names(CurrentL) <- unique(UniMachine)
tempM <- aggregate(tempI,list(UniMachine),median,na.rm = T)
temp <- aggregate(tempI,list(UniMachine),function(x){
# x <<- x
tempDens <- list(x = 0,y = 0)
tempi <- class(try(tempDens <- density(x,na.rm = T),silent = T))
tempDens$Quantile <- quantile(x,prob = c(0.75,0.95,0.5,0.25,0.05),na.rm = T)
if(tempi!="try-error"){
tempDens$y <- tempDens$y /max(tempDens$y,na.rm = T)
}
return(tempDens)}
)
OrderFun <- merge.control(temp$Group.1,LegFun$Mac)
xlim <- range(tempI[!is.infinite(tempI)],na.rm = T)
if(!any(c(is.na(xlim),is.infinite(xlim)))){
plot(1,type = "n",ylim = c(0,1),xlim =xlim ,xlab = "",main = tempDensMatrix[a,2],ylab = "",frame = F)
}else{
plot(1,type = "n",ylim = c(0,1) ,xlab = "",main = tempDensMatrix[a,2],ylab = "",frame = F)
}
itCompare <<- 0
# pointsList <<- list()
pointsList <- sapply(OrderFun,function(x){
itCompare <<- itCompare+1
if(is.matrix(temp$x)){
subDens <- temp$x[x,]
}else{
subDens <- temp$x[[x]]
}
if(exists("subDens")){
try(subDens$y <- subDens$y /max(subDens$y ))
trye <- class(try(points(subDens,col = LegFun$col[itCompare],lty = 1,type = "l",lwd = LegFun$lwd),silent = T))
Current <- CurrentL[[itCompare]]
CurrentDiff <- abs(subDens$x-as.numeric(Current[1]))
Currenty <- subDens$y[CurrentDiff == min(CurrentDiff,na.rm = T)]
Currenty <- Currenty[!is.na(Currenty)]
if(length(Currenty)==0){Currenty <- NA}
pointsList<- c(as.numeric(Current[1]),Currenty,col = LegFun$col[itCompare],pch = LegFun$pch[itCompare],subDens$Quantile)
# try(points())
if(trye!="try-error"){
try(xl<- median(tempM[x,2],na.rm = T),silent = T)
#abline(v = xl<- median(tempM[x,2],na.rm = T),col = LegFun$col[x],lty = "dotted")
try(subvec <- abs(xl -subDens$x) ,silent = T)
try(yl <- subDens$y[subvec == min(subvec,na.rm = T)][1],silent = T)
try(lines(c(xl,xl),c(0,yl),col = LegFun$col[itCompare],lty = "dotted"),silent =T)
try(axis(1,at = xl,col = LegFun$col[itCompare],label = ""),silent = T)
}
}else{ pointsList<- c(Current,rep(NA,9))
}
return(pointsList)
})
# pointsList <<-pointsList
apply(pointsList,2,function(x){
try(points(x[1],x[2],bg = "white",col = "white",pch = 23,cex = 1.85,lwd = 0.5),silent = T)
return(NULL)
})
apply(pointsList,2,function(x){
try(points(x[1],x[2],col = x[3],pch = as.numeric(x[4]),cex = 1,xpd = NA),silent = F)
return(NULL)
})
pointsList <- pointsList[grep("%",rownames(pointsList)),]
try(colnames(pointsList) <- LegFun$Mac,silent = T) # check if naming is correct
PointsListQuantiles[[itMain]] <- pointsList
}else{
plot(1,type = "n",ylim = c(0,1),xlab = "",main = tempDensMatrix[a,2],ylab = "",frame = F)
}
}
}
naQuan <- c(naQuan,tempDensMatrix[,1])
}
names(PointsListQuantiles)<- naQuan
par(mai = rep(0,4),mar = rep(0,4))
empty.plot()
# CurrentL <<- CurrentL
CL <- sapply(CurrentL,function(x){x[2]})
names(CL) <- names(CurrentL)
CL <- CL[match(names(CL),as.character(LegFun$Mac))]
# LegFun <<- LegFun
legend("left"
,legend = paste(as.character(LegFun$Mac),CL,sep = "\n")
,col = as.character(LegFun$col)
,lwd = LegFun$lwd,
,border = "transparent",box.col = "transparent",bg = "#FFFFFF80",xpd = NA,y.intersp = 2
)
legend("topright",legend = Sys.Date(),bty = "n")
graphics.off()
if(pdfShow){
try(system(paste("open",pdfName)))
}
# system(paste("open",pdfName))
# LoadSettings(inputframe = tempListOne,DensMatrixTemplate = DensMatrixTemplate,pdfname = paste(finalMQQC ,"TimeLines", paste("Correlations",PDFname,sep = "_"),sep = "/"),pdfshow = F)
cat("\rPreparing Timelines")
try(PairsFun(inputframe = tempListOne,DensMatrixTemplate = DensMatrixTemplate,pdfname = paste(finalMQQC ,"TimeLines", paste("Correlations",PDFname,sep = "_"),sep = "/"),pdfshow = F),silent = T)
return(PointsListQuantiles)
}
# try(trash <-CompareComplexStdFromTable(collectList[ECstd,],RESettings,F,finalMQQC, PDFname = "ComplexStandardComparison.jpg", TargetVec = StandardIDs[1],PDF = F, Machines = Machines),silent = T)
# try(RestQuan <- CompareComplexStdFromTable(collectList[Normal,],RESettings,F,finalMQQC, PDFname = "NormalSampleComparison.pdf",main = "MQQC Normal Samples Parameter Comparison", TargetVec = "",PDF = T, Machines = Machines,pdfShow = T),silent = F)
# try(trash <-CompareComplexStdFromTable(tempListOne = collectList[ECstd,],RESettings = RESettings,pdfShow = T,finalMQQC = finalMQQC, PDFname = "ComplexStandardComparison.pdf", TargetVec = StandardIDs[1],PDF = T, Machines = Machines),silent = F)
# try(ECquan <- CompareComplexStdFromTable(tempListOne = collectList[ECstd,],RESettings = RESettings,finalMQQC = finalMQQC, PDFname = "ComplexStandardComparison.jpg", TargetVec = StandardIDs[1],PDF = F, Machines = unique(strsplitslot(unique(tempListOne$Name),1,"_",fixed = T)),StandardIDs = StandardIDs,pdfShow = T),silent = F)
# try(ECquan <- CompareComplexStdFromTable(tempListOne = collectList[ECstd,],pdfShow = T,RESettings = RESettings,finalMQQC = finalMQQC, PDFname = "ComplexStandardComparison.pdf", TargetVec = StandardIDs[1],PDF = T, Machines = Machines,StandardIDs = StandardIDs),silent = T)
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