Nothing
R/plot.profile.R
In mqqc: Quality control of LCMS derived proteomic data
Defines functions
plot.profile
plot.profile <-
function(data.i,layout = T,linePlot =F,BSACheck = F, plot.legend = T,ProtFDR = 0.01,funfun = NULL,msScans = NULL,msmsScans = NULL,addDensities = T){
data.i$reverse[is.na(data.i$reverse)] <- ""
AllDensCol <- colors()[235]
IntQuanDensCol <- "lightblue"#colors()[57] #632
plotData <- list()
if(layout){
layout(matrix(c(1,2,3,4),ncol = 2,nrow = 2),height = c(5,1.5),width = c(5,1))
par(mai=c(0,1,0.1,0))
}
colnames(data.i) <- tolower(colnames(data.i))
data.i$m.z[data.i$reverse == "+"] <- NA
data.i <- data.i[data.i$reverse != "+",]
data.i$potential.contaminant[is.na(data.i$potential.contaminant)] <- ""
data.i <<- data.i
if(BSACheck){
BSAEVI <- data.i[BSAgrep <- grep("P02769",data.i$proteins),]
}
name.file <- unique(data.i$raw.file)#"Elutionprofile"
######
# Chromatography test
######
# modify intensity
Ramp.col <- colorRampPalette(c("dodgerblue2","blue","darkblue","navyblue"))(101)
BSA.col <- colorRampPalette(c("#fca502","red","darkred","violet"))(101)
CON.col <- colorRampPalette(c("#fca502","red","darkred","violet"))(101)
data.i$retention.time <- as.numeric(data.i$retention.time)
data.i$m.z <- as.numeric(data.i$m.z)
data.i$intensity <- as.numeric(data.i$intensity)
intensity <- as.numeric(data.i$intensity)
intensity <- intensity/max(intensity,na.rm = T)*100
intensity[is.na(intensity)] <- 1
if(BSACheck){
Ramp.col.BSA <- BSA.col[(round(intensity)+1)[BSAgrep]]
}
Ramp.col <- Ramp.col[(round(intensity,1)+1)]
Ramp.col[data.i$potential.contaminant == "+"] <- "#fca502"
if(BSACheck){
Ramp.col[BSAgrep] <- Ramp.col.BSA
}else{
Ramp.col[data.i$potential.contaminant == "+"] <- CON.col[(round(intensity)+1)[data.i$potential.contaminant == "+"]]
}
intensity <- intensity/100*5
intensity[is.na(intensity)] <- 0
intensity <- sqrt(intensity)
intensity <- round(intensity,1)*1.5
Ramp.col[is.na(Ramp.col)] <- "grey"
col.intensity <- grep("intensity",tolower(colnames(data.i)))
plotData$profile <- cbind(data.i$retention.time,data.i$m.z)
plot(data.i$retention.time,data.i$m.z,pch = 20,cex = intensity,col = Ramp.col,type = "n" ,ylab = "m/z",xlim = xl <- range(data.i$retention.time,na.rm = T),axes = F,ylim = range(data.i$m.z,na.rm = T),frame = F)
abline(v=median(data.i$retention.time),col = "#00000060",lwd = 1)
quantiles <- quantile(data.i$retention.time,na.rm =T)
abline(v= quantiles[c(2,4)],col = IntQuanDensCol,lty = c("dashed","solid"),lwd = 1)
abline(h=median(data.i$m.z),col = "#00000060",lwd = 1)
quantiles <- quantile(data.i$m.z,na.rm = T)
abline(h= quantiles[c(2,4)],col = IntQuanDensCol,lty = c("dashed","solid"),lwd = 1)
# mtext("MS1\nintensity",1,cex = 0.6,las = 2)
axis(2,tck = -0.015)
axis(1,labels = F,tck = -0.015)
uniqueSeq <- length(unique(data.i$sequence))
intens <- quantile(as.numeric(data.i$intensity[!is.na(data.i$intensity)]))
intens <- paste("Intensities Q 0.5-1 :",format(intens[3],digits = 3, scientific = T),format(intens[5],digits =3, scientific = T))
if(BSACheck){
name.file <- c(as.character(name.file), paste("BSA peptides:",length(grep("MSMS",BSAEVI$type)),", all peptides:",length(grep("MSMS",data.i$type))),intens)
}else{
data.u <<- data.i
sel <- data.i$q.value < 0.01
if(length(sel) == 0){
sel <- rep(T,dim(data.i)[1])
}
pepPu<- aggregate(as.numeric(data.i$pep),list(data.i$leading.razor.protein,data.i$sequence),min,na.rm = T)
pepPr <- aggregate(pepPu$x,list(pepPu$Group.1),prod)
pepPr <- pepPr[order(pepPr[,2]),]
Rev <- grep("^REV",pepPr[,1])
if(length(Rev) > 0){
RevP <- (1:length(Rev))/Rev
hum <- Rev-c(0,Rev[-length(Rev)])
# hum[length(hum)] <- 0
fu <- unlist(apply(cbind(hum,RevP),1,function(x){return(rep(x[2],x[1]))}))
PL <- length(fu[fu < ProtFDR])
}else{
PL <- dim(pepPr)[1]
}
name.file <- c(as.character(name.file), paste("Proteins:",PL),paste("Peptides, all:",length(grep("MSMS",data.i$type)),", unique:",uniqueSeq),intens)
}
grid(col = "darkgrey",lwd = 1.5)
if(plot.legend){
legend("topleft",legend = name.file,bg = "white",box.col = "transparent")
}
tempBorder <- densCols(data.i$retention.time,data.i$m.z,colramp = colorRampPalette(c("white","darkgrey")))
# tempBorder[data.i$Potential.contaminant == "+"] <- "#fca502"
for(i in 1:length(unique(Ramp.col))){
mFac <- diff(yrange<- range(as.numeric(data.i$m.z),na.rm = T))/250
temp.i.sel <- Ramp.col == unique(Ramp.col)[i]
x <- data.i$retention.time[temp.i.sel]
y <- data.i$m.z[temp.i.sel]
Start <- as.numeric(data.i$calibrated.retention.time.start[temp.i.sel])
Finish <- as.numeric(data.i$calibrated.retention.time.finish[temp.i.sel])
tempBorderi <- tempBorder[temp.i.sel]
# x <<- x
# y <<- y
if(any(length(Start)== 0|length(Finish) == 0)){
Start <- y -1
Finish <- y +1
.border <- "grey"
}else{
.border <- "lightgrey"
}
.border = tempBorderi
.cols <- unique(Ramp.col)[i]
if(linePlot){
tempM <- cbind(Start ,Finish,x,y)
itm <<- 1
apply(tempM,1,function(x){
xPoly <- c(x[1],x[3],x[2],x[3],x[1] )
yPoly <- c(x[4],x[4]+mFac,x[4],x[4]-mFac,x[4])
try( polygon(xPoly,yPoly,col = .cols,border = .border[itm],lwd = 0.3))
itm <<- itm+1
})
}else{
points(x,y,pch = 20,cex = intensity[temp.i.sel],col = Ramp.col[temp.i.sel] )
}
}
if(BSACheck){
BSAx <- as.numeric(data.i$retention.time[BSAgrep])
BSAy <- as.numeric(data.i$m.z[BSAgrep])
BSAmz <- round(BSAy,1)
text(BSAx,BSAy,BSAmz,pos = 3,cex = 0.4)
}
if(addDensities){
if(length(funfun) == 0&exists("msScans")){
par(mai=c(0.6,1,0.1,0))
}else{
par(mai=c(0.1,1,0.1,0))
}
data.i$potential.contaminant[is.na(data.i$potential.contaminant)] <- ""
pcon <- data.i$potential.contaminant == "+"
if(any(pcon)){
dens.conA <- createWindows(as.numeric(data.i$retention.time)[pcon])$full
}else{dens.conA <- NULL}
dens.crtA <- createWindows(as.numeric(data.i$retention.time)[!pcon])$full
dens.crtA0 <- dens.crtA[dens.crtA !=0]
nofa <- max(medwin(as.numeric(names(dens.crtA0)),dens.crtA0/max(as.numeric(dens.crtA0)))$y)
densityRescale <- T
if(!densityRescale){
nofa <- 1
}
dens.crt <- class(try(temp <- density(DAT <- as.numeric(data.i$retention.time),na.rm = T)))
tempCON <- NULL
dens.con <- class(try(tempCON <- density(CON <- as.numeric(data.i$retention.time)[data.i$potential.contaminant == "+"],na.rm = T)))
temp$y <- temp$y/max(temp$y,na.rm = T)*nofa
tempCON$y <- tempCON$y/max(tempCON$y,na.rm = T)
try(ConFAC <- length(CON)/length(DAT))
try(tempCON$y <- tempCON$y * ConFAC)
if(dens.crt == "try-error"){temp <- list(x=0,y=0)}
plotData$retentionTime <- cbind(temp$x,temp$y)
plot(temp$x,temp$y,main = "",axes = F,frame = F,xlim = range(as.numeric(data.i$retention.time),na.rm = T),type = "n",xlab = "",ylab = "",lwd = 1,ylim = c(0,1))
# grid(col = "darkgrey",lwd = 1.5)
abline(v = pretty(temp$x),col = "darkgrey",lwd = 1.5,lty = "dotted")
quantiles <- quantile(data.i$retention.time,na.rm = T)
abline(v= quantiles[c(2,4)],col = IntQuanDensCol,lty = c("dashed","solid"),lwd = 1)
#points(temp$x,temp$y,main = "",axes = F,frame = F,xlim = range(data.i$retention.time,na.rm = T),type = "l",xlab = "",ylab = "",lwd = 2,col = "grey30")
polygon(temp$x,temp$y,col = AllDensCol,border = AllDensCol)
Inner <- temp$x <= quantiles[4] & temp$x >= quantiles[2]
pX <- temp$x[Inner]
pY <- temp$y[Inner]
polygon(c(min(pX),pX,max(pX)),c(0,pY,0),col = IntQuanDensCol,border = IntQuanDensCol)
abline(v=median(data.i$retention.time),col = "white",lwd = 2)
if(length(funfun) == 0){
mtext("time in min",1,line = 1.9,cex = 0.6)
#axis(2,xpd = NA,las = 2)
axis(1)
}
mtext("identified\nMS2\ncounts",2,cex = 0.6,las = 2)
if(!(length(funfun) > 0 & exists("msScans"))){
mtext("time in min",1,line = 1.9,cex = 0.6)
#axis(2,xpd = NA,las = 2)
axis(1)
abline(v= quantiles[c(2,4)],col = IntQuanDensCol,lty = c("dashed","solid"),lwd = 1)
}
if(BSACheck){
BSAdensFactor <- length(BSAgrep)/dim(data.i)[1]
dens.crt <- class(try(temp <- density(data.i$retention.time[BSAgrep])))
if(dens.crt == "try-error"){temp <- list(x=0,y=0)}
plotData$BSAretentionTime <- cbind(temp$x,temp$y)
# points(temp$x,temp$y* BSAdensFactor,type = "l",col = "white",lwd = 4)
# points(temp$x,temp$y* BSAdensFactor,main = "",xlim = range(data.i$retention.time[BSAgrep],na.rm = T),type = "l",xlab = "",ylab = "Density",col = "#fca502",lwd = 3)
# mtext("time in min",1,line = 1.9,cex = 0.6)
# try(legend("topright",legend = c("all","BSA"),col = c(AllDensCol,"#fca502"),bg = c(AllDensCol,"#fca502"),pch = 17,bty = "n",cex = 0.5))
try(plotPOL(names(dens.conA),dens.conA/max(dens.crtA),col = "#fca50280",type = "l",border = "transparent"),silent = T)
}else{
# ConFAC <<- ConFAC
if(log2(ConFAC) > -4){
# try(points(tempCON$x,tempCON$y,type = "l",col = "#fca502",lwd = 2,lty = "dotted"))
try(plotPOL(names(dens.conA),dens.conA/max(dens.crtA),col = "#fca50280",type = "l",border = "transparent"),silent = T)
# try(legend("topright",legend = c("all","contaminants"),col = c(AllDensCol,"#fca502"),bg = c(AllDensCol,"#fca502"),pch = 17,bty = "n",cex = 0.5))
#points(tempCON$x,tempCON$y,main = "",axes = F,frame = F,na.rm = T,type = "l",xlab = "",ylab = "Density",col = "dark#fca502",lwd = 3)
# try(legend("topright",legend = c("contaminants"),col = c("grey"),lty = "dotted",lwd = 3,bty = "n"))
}
}
plotPOL(names(dens.crtA),dens.crtA/max(dens.crtA),col = "#99999990",type = "l",border = "transparent")
try(dens.mzCA <- (createWindows(data.i$m.z[data.i$potential.contaminant == "+"])$full))
dens.mzA <- (createWindows(data.i$m.z[data.i$potential.contaminant != "+"])$full)
dens.crt <- class(try( temp <-density(data.i$m.z)))
dens.mzA0 <- dens.mzA[dens.mzA !=0]
nofa <- max(medwin(as.numeric(names(dens.mzA0)),dens.mzA0/max(dens.mzA0))$y)
densityRescale <- T
if(!densityRescale){
nofa <- 1
}
temp$y <- temp$y/max(temp$y)*nofa
if(dens.crt == "try-error"){temp <- list(x=0,y=0)}
#
par(mai=c(0,0,0.1,0.1))
plotData$mz <- cbind(temp$x,temp$y)
plot(temp$y,temp$x,type = "n",axes = F,frame = F,ylim = range(c(data.i$m.z),na.rm = T),xlim = c(0,1),xlab = "Density",ylab = "",lwd = 1,col = "white")
# grid(col = "darkgrey",lwd = 1.5)
abline(h = pretty(temp$y),col = "darkgrey",lwd = 1.5,lty = "dotted")
quantiles <- quantile(data.i$m.z,na.rm =T)
#abline(h= quantiles[c(2,4)],col = IntQuanDensCol,lty = c("dashed","solid"),lwd = 1)
#points(temp$y,temp$x,type = "l",axes = F,frame = F,ylim = range(data.i$m.z,na.rm = T),xlab = "Density",ylab = "",lwd = 1,col = "grey30")
polygon(temp$y,temp$x,col = AllDensCol,border = AllDensCol)
Inner <- temp$x <= quantiles[4] & temp$x >= quantiles[2]
pX <- temp$x[Inner]
pY <- temp$y[Inner]
try(polygon(c(0,pY,0),c(min(pX),pX,max(pX)),col = IntQuanDensCol,border = IntQuanDensCol))
abline(h=median(data.i$m.z),col = "white",lwd = 2)
#axis(1,xpd = NA,las = 2)
#mtext("Density",1,line = 4,cex = 0.6)
if(BSACheck){
dens.crt <- class(try( temp <-density(data.i$m.z[BSAgrep])))
if(dens.crt == "try-error"){temp <- list(x=0,y=0)}
# par(mai=c(0,0,0.1,0.1))
# try( points(temp$y*BSAdensFactor,temp$x,type = "l",frame = F,ylim = range(data.i$m.z,na.rm = T),xlab = "Density",ylab = "",col = "white",lwd = 4))
# try( points(temp$y*BSAdensFactor,temp$x,type = "l",frame = F,ylim = range(data.i$m.z,na.rm = T),xlab = "Density",ylab = "",col = "#fca502",lwd = 3))
# try(legend("topright",legend = c("all","BSA"),col = c(AllDensCol,"#fca502"),bg = c(AllDensCol,"#fca502"),pch = 17,bty = "n",cex = 0.5))
}else{
# try(legend("topright",legend = c("all","con-\ntami-\nnants"),col = c(AllDensCol,"#fca502"),bg = c(AllDensCol,"#fca502"),pch = 17,bty = "n",cex = 0.5))
}
if(log2(ConFAC) > -4){
# try(points(tempCON$x,tempCON$y,type = "l",col = "#fca502",lwd = 2,lty = "dotted"))
try(plotPOL(a <- unfactor(dens.mzCA/max(c(dens.mzA,dens.mzCA))),b <- as.numeric(names(dens.mzCA)),col = "#fca50280",type = "p",border = "transparent"))
# points(dens.mzA/max(c(dens.mzA,dens.mzCA)),as.numeric(names(dens.mzA)),col = "#99999990",type = "h",border = "transparent")
#points(tempCON$x,tempCON$y,main = "",axes = F,frame = F,na.rm = T,type = "l",xlab = "",ylab = "Density",col = "dark#fca502",lwd = 3)
# try(legend("topright",legend = c("contaminants"),col = c("grey"),lty = "dotted",lwd = 3,bty = "n"))
}
try(plotPOL(a <- unfactor(dens.mzA/max(c(dens.mzA,dens.mzCA))),b <- as.numeric(names(dens.mzA)),col = "#99999990",type = "p",border = "transparent"))
# axis(2,xpd = NA,labels = F,padj = 0.5,tck = 0.04)
par(mai = c(0,0,0,0))
plot(1,type = "n",frame = F,axes = F)
if(BSACheck){
# try( points(temp$y*BSAdensFactor,temp$x,type = "l",frame = F,ylim = range(data.i$m.z,na.rm = T),xlab = "Density",ylab = "",col = "white",lwd = 4))
# try( points(temp$y*BSAdensFactor,temp$x,type = "l",frame = F,ylim = range(data.i$m.z,na.rm = T),xlab = "Density",ylab = "",col = "#fca502",lwd = 3))
try(legend("topleft",legend = c("other","BSA"),title = "Peptides",col = c(AllDensCol,"#fca502"),bg = c(AllDensCol,"#fca502"),pch = 17,bty = "n",cex = 0.5))
}else{
try(legend("topleft",legend = c("other","contaminants"),title = "Peptides",col = c(AllDensCol,"#fca502"),bg = c(AllDensCol,"#fca502"),pch = 17,bty = "n",cex = 0.5))
}
plotData$name.file <- name.file
if(length(funfun) > 0 & exists("msScans")){
par(mai=c(0.8,1,0,0))
try(funfun(msScans = msScans,msmsScans = msmsScans,xl = xl))
mtext("time in min",1,line = 1.9,cex = 0.6)
#axis(2,xpd = NA,las = 2)
axis(1)
abline(v= quantiles[c(2,4)],col = IntQuanDensCol,lty = c("dashed","solid"),lwd = 1)
}else{
mtext("time in min",1,line = 1.9,cex = 0.6)
#axis(2,xpd = NA,las = 2)
axis(1)
abline(v= quantiles[c(2,4)],col = IntQuanDensCol,lty = c("dashed","solid"),lwd = 1)
empty.plot()
}
print("Finished Plotting Scores")
}
return(plotData)
}
# sink(
# )
# sink()
# library(mqqc)
# graphics.off()
# pdf("test.pdf")
# path <- "/Users/henno/temp/mqqc/_RmqqcFile_Old/Test2/Beaker_20180219_OP_HSstd_Px08_HeLa_100ng_MQQCreanalyzedraw_folder - Copy/combined/txt/evidence.txt"
# temp <- read.csv(path,sep = "\t",stringsAsFactors = F)
# table(temp$raw.file)
# colnames(temp) <- tolower(colnames(temp))
# plot.profile(temp,linePlot = T,plot.legend = F,layout = F,addDensities = F)
# dev.off()
# system("open test.pdf")
# tryError2 <- class(try(TotalScoreRes <- plot.scores(data.i = temp.DataEvidence,msScans = msScans,msmsScans= msmsScans,data.list = qc.prepare.data,pdf.name = i, open.doc = open.doc,pdfOut = pdfOut, BSACheck = BSACheck)))
# tryError2 <- class(try(TotalScoreRes <- plot.scores(data.i = temp.DataEvidence,msScans = msScans,msmsScans= msmsScans,data.list = qc.prepare.data,pdf.name = i, open.doc = T,pdfOut = pdfOut, BSACheck = BSACheck)))
# plotMsFun <- NULL
# tryError2 <- class(try(TotalScoreRes <- plot.scores(data.i = temp.DataEvidence,msScans = NULL,msmsScans= NULL,data.list = qc.prepare.data,pdf.name = i, open.doc = T,pdfOut = pdfOut, BSACheck = BSACheck)))
# plot.profile(data.i,linePlot = T)
#try(plotData<- plot.profile(data.i,T,dots,BSACheck= BSACheck,plot.legend = F))
#plot.profile(temp.DataEvidence)
#tryError2 <- class(try(TotalScoreRes <- plot.scores(data.i = temp.DataEvidence,data.list = qc.prepare.data,pdf.name = i, open.doc = T,pdfOut = pdfOut, BSACheck = BSACheck)))
#par(mfrow = c(2,2))
#try(plotData<- plot.profile(data.i,F,F,BSACheck= T))
#plot.profile(Data)
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Defines functions plot.profile
plot.profile <-
function(data.i,layout = T,linePlot =F,BSACheck = F, plot.legend = T,ProtFDR = 0.01,funfun = NULL,msScans = NULL,msmsScans = NULL,addDensities = T){
data.i$reverse[is.na(data.i$reverse)] <- ""
AllDensCol <- colors()[235]
IntQuanDensCol <- "lightblue"#colors()[57] #632
plotData <- list()
if(layout){
layout(matrix(c(1,2,3,4),ncol = 2,nrow = 2),height = c(5,1.5),width = c(5,1))
par(mai=c(0,1,0.1,0))
}
colnames(data.i) <- tolower(colnames(data.i))
data.i$m.z[data.i$reverse == "+"] <- NA
data.i <- data.i[data.i$reverse != "+",]
data.i$potential.contaminant[is.na(data.i$potential.contaminant)] <- ""
data.i <<- data.i
if(BSACheck){
BSAEVI <- data.i[BSAgrep <- grep("P02769",data.i$proteins),]
}
name.file <- unique(data.i$raw.file)#"Elutionprofile"
######
# Chromatography test
######
# modify intensity
Ramp.col <- colorRampPalette(c("dodgerblue2","blue","darkblue","navyblue"))(101)
BSA.col <- colorRampPalette(c("#fca502","red","darkred","violet"))(101)
CON.col <- colorRampPalette(c("#fca502","red","darkred","violet"))(101)
data.i$retention.time <- as.numeric(data.i$retention.time)
data.i$m.z <- as.numeric(data.i$m.z)
data.i$intensity <- as.numeric(data.i$intensity)
intensity <- as.numeric(data.i$intensity)
intensity <- intensity/max(intensity,na.rm = T)*100
intensity[is.na(intensity)] <- 1
if(BSACheck){
Ramp.col.BSA <- BSA.col[(round(intensity)+1)[BSAgrep]]
}
Ramp.col <- Ramp.col[(round(intensity,1)+1)]
Ramp.col[data.i$potential.contaminant == "+"] <- "#fca502"
if(BSACheck){
Ramp.col[BSAgrep] <- Ramp.col.BSA
}else{
Ramp.col[data.i$potential.contaminant == "+"] <- CON.col[(round(intensity)+1)[data.i$potential.contaminant == "+"]]
}
intensity <- intensity/100*5
intensity[is.na(intensity)] <- 0
intensity <- sqrt(intensity)
intensity <- round(intensity,1)*1.5
Ramp.col[is.na(Ramp.col)] <- "grey"
col.intensity <- grep("intensity",tolower(colnames(data.i)))
plotData$profile <- cbind(data.i$retention.time,data.i$m.z)
plot(data.i$retention.time,data.i$m.z,pch = 20,cex = intensity,col = Ramp.col,type = "n" ,ylab = "m/z",xlim = xl <- range(data.i$retention.time,na.rm = T),axes = F,ylim = range(data.i$m.z,na.rm = T),frame = F)
abline(v=median(data.i$retention.time),col = "#00000060",lwd = 1)
quantiles <- quantile(data.i$retention.time,na.rm =T)
abline(v= quantiles[c(2,4)],col = IntQuanDensCol,lty = c("dashed","solid"),lwd = 1)
abline(h=median(data.i$m.z),col = "#00000060",lwd = 1)
quantiles <- quantile(data.i$m.z,na.rm = T)
abline(h= quantiles[c(2,4)],col = IntQuanDensCol,lty = c("dashed","solid"),lwd = 1)
# mtext("MS1\nintensity",1,cex = 0.6,las = 2)
axis(2,tck = -0.015)
axis(1,labels = F,tck = -0.015)
uniqueSeq <- length(unique(data.i$sequence))
intens <- quantile(as.numeric(data.i$intensity[!is.na(data.i$intensity)]))
intens <- paste("Intensities Q 0.5-1 :",format(intens[3],digits = 3, scientific = T),format(intens[5],digits =3, scientific = T))
if(BSACheck){
name.file <- c(as.character(name.file), paste("BSA peptides:",length(grep("MSMS",BSAEVI$type)),", all peptides:",length(grep("MSMS",data.i$type))),intens)
}else{
data.u <<- data.i
sel <- data.i$q.value < 0.01
if(length(sel) == 0){
sel <- rep(T,dim(data.i)[1])
}
pepPu<- aggregate(as.numeric(data.i$pep),list(data.i$leading.razor.protein,data.i$sequence),min,na.rm = T)
pepPr <- aggregate(pepPu$x,list(pepPu$Group.1),prod)
pepPr <- pepPr[order(pepPr[,2]),]
Rev <- grep("^REV",pepPr[,1])
if(length(Rev) > 0){
RevP <- (1:length(Rev))/Rev
hum <- Rev-c(0,Rev[-length(Rev)])
# hum[length(hum)] <- 0
fu <- unlist(apply(cbind(hum,RevP),1,function(x){return(rep(x[2],x[1]))}))
PL <- length(fu[fu < ProtFDR])
}else{
PL <- dim(pepPr)[1]
}
name.file <- c(as.character(name.file), paste("Proteins:",PL),paste("Peptides, all:",length(grep("MSMS",data.i$type)),", unique:",uniqueSeq),intens)
}
grid(col = "darkgrey",lwd = 1.5)
if(plot.legend){
legend("topleft",legend = name.file,bg = "white",box.col = "transparent")
}
tempBorder <- densCols(data.i$retention.time,data.i$m.z,colramp = colorRampPalette(c("white","darkgrey")))
# tempBorder[data.i$Potential.contaminant == "+"] <- "#fca502"
for(i in 1:length(unique(Ramp.col))){
mFac <- diff(yrange<- range(as.numeric(data.i$m.z),na.rm = T))/250
temp.i.sel <- Ramp.col == unique(Ramp.col)[i]
x <- data.i$retention.time[temp.i.sel]
y <- data.i$m.z[temp.i.sel]
Start <- as.numeric(data.i$calibrated.retention.time.start[temp.i.sel])
Finish <- as.numeric(data.i$calibrated.retention.time.finish[temp.i.sel])
tempBorderi <- tempBorder[temp.i.sel]
# x <<- x
# y <<- y
if(any(length(Start)== 0|length(Finish) == 0)){
Start <- y -1
Finish <- y +1
.border <- "grey"
}else{
.border <- "lightgrey"
}
.border = tempBorderi
.cols <- unique(Ramp.col)[i]
if(linePlot){
tempM <- cbind(Start ,Finish,x,y)
itm <<- 1
apply(tempM,1,function(x){
xPoly <- c(x[1],x[3],x[2],x[3],x[1] )
yPoly <- c(x[4],x[4]+mFac,x[4],x[4]-mFac,x[4])
try( polygon(xPoly,yPoly,col = .cols,border = .border[itm],lwd = 0.3))
itm <<- itm+1
})
}else{
points(x,y,pch = 20,cex = intensity[temp.i.sel],col = Ramp.col[temp.i.sel] )
}
}
if(BSACheck){
BSAx <- as.numeric(data.i$retention.time[BSAgrep])
BSAy <- as.numeric(data.i$m.z[BSAgrep])
BSAmz <- round(BSAy,1)
text(BSAx,BSAy,BSAmz,pos = 3,cex = 0.4)
}
if(addDensities){
if(length(funfun) == 0&exists("msScans")){
par(mai=c(0.6,1,0.1,0))
}else{
par(mai=c(0.1,1,0.1,0))
}
data.i$potential.contaminant[is.na(data.i$potential.contaminant)] <- ""
pcon <- data.i$potential.contaminant == "+"
if(any(pcon)){
dens.conA <- createWindows(as.numeric(data.i$retention.time)[pcon])$full
}else{dens.conA <- NULL}
dens.crtA <- createWindows(as.numeric(data.i$retention.time)[!pcon])$full
dens.crtA0 <- dens.crtA[dens.crtA !=0]
nofa <- max(medwin(as.numeric(names(dens.crtA0)),dens.crtA0/max(as.numeric(dens.crtA0)))$y)
densityRescale <- T
if(!densityRescale){
nofa <- 1
}
dens.crt <- class(try(temp <- density(DAT <- as.numeric(data.i$retention.time),na.rm = T)))
tempCON <- NULL
dens.con <- class(try(tempCON <- density(CON <- as.numeric(data.i$retention.time)[data.i$potential.contaminant == "+"],na.rm = T)))
temp$y <- temp$y/max(temp$y,na.rm = T)*nofa
tempCON$y <- tempCON$y/max(tempCON$y,na.rm = T)
try(ConFAC <- length(CON)/length(DAT))
try(tempCON$y <- tempCON$y * ConFAC)
if(dens.crt == "try-error"){temp <- list(x=0,y=0)}
plotData$retentionTime <- cbind(temp$x,temp$y)
plot(temp$x,temp$y,main = "",axes = F,frame = F,xlim = range(as.numeric(data.i$retention.time),na.rm = T),type = "n",xlab = "",ylab = "",lwd = 1,ylim = c(0,1))
# grid(col = "darkgrey",lwd = 1.5)
abline(v = pretty(temp$x),col = "darkgrey",lwd = 1.5,lty = "dotted")
quantiles <- quantile(data.i$retention.time,na.rm = T)
abline(v= quantiles[c(2,4)],col = IntQuanDensCol,lty = c("dashed","solid"),lwd = 1)
#points(temp$x,temp$y,main = "",axes = F,frame = F,xlim = range(data.i$retention.time,na.rm = T),type = "l",xlab = "",ylab = "",lwd = 2,col = "grey30")
polygon(temp$x,temp$y,col = AllDensCol,border = AllDensCol)
Inner <- temp$x <= quantiles[4] & temp$x >= quantiles[2]
pX <- temp$x[Inner]
pY <- temp$y[Inner]
polygon(c(min(pX),pX,max(pX)),c(0,pY,0),col = IntQuanDensCol,border = IntQuanDensCol)
abline(v=median(data.i$retention.time),col = "white",lwd = 2)
if(length(funfun) == 0){
mtext("time in min",1,line = 1.9,cex = 0.6)
#axis(2,xpd = NA,las = 2)
axis(1)
}
mtext("identified\nMS2\ncounts",2,cex = 0.6,las = 2)
if(!(length(funfun) > 0 & exists("msScans"))){
mtext("time in min",1,line = 1.9,cex = 0.6)
#axis(2,xpd = NA,las = 2)
axis(1)
abline(v= quantiles[c(2,4)],col = IntQuanDensCol,lty = c("dashed","solid"),lwd = 1)
}
if(BSACheck){
BSAdensFactor <- length(BSAgrep)/dim(data.i)[1]
dens.crt <- class(try(temp <- density(data.i$retention.time[BSAgrep])))
if(dens.crt == "try-error"){temp <- list(x=0,y=0)}
plotData$BSAretentionTime <- cbind(temp$x,temp$y)
# points(temp$x,temp$y* BSAdensFactor,type = "l",col = "white",lwd = 4)
# points(temp$x,temp$y* BSAdensFactor,main = "",xlim = range(data.i$retention.time[BSAgrep],na.rm = T),type = "l",xlab = "",ylab = "Density",col = "#fca502",lwd = 3)
# mtext("time in min",1,line = 1.9,cex = 0.6)
# try(legend("topright",legend = c("all","BSA"),col = c(AllDensCol,"#fca502"),bg = c(AllDensCol,"#fca502"),pch = 17,bty = "n",cex = 0.5))
try(plotPOL(names(dens.conA),dens.conA/max(dens.crtA),col = "#fca50280",type = "l",border = "transparent"),silent = T)
}else{
# ConFAC <<- ConFAC
if(log2(ConFAC) > -4){
# try(points(tempCON$x,tempCON$y,type = "l",col = "#fca502",lwd = 2,lty = "dotted"))
try(plotPOL(names(dens.conA),dens.conA/max(dens.crtA),col = "#fca50280",type = "l",border = "transparent"),silent = T)
# try(legend("topright",legend = c("all","contaminants"),col = c(AllDensCol,"#fca502"),bg = c(AllDensCol,"#fca502"),pch = 17,bty = "n",cex = 0.5))
#points(tempCON$x,tempCON$y,main = "",axes = F,frame = F,na.rm = T,type = "l",xlab = "",ylab = "Density",col = "dark#fca502",lwd = 3)
# try(legend("topright",legend = c("contaminants"),col = c("grey"),lty = "dotted",lwd = 3,bty = "n"))
}
}
plotPOL(names(dens.crtA),dens.crtA/max(dens.crtA),col = "#99999990",type = "l",border = "transparent")
try(dens.mzCA <- (createWindows(data.i$m.z[data.i$potential.contaminant == "+"])$full))
dens.mzA <- (createWindows(data.i$m.z[data.i$potential.contaminant != "+"])$full)
dens.crt <- class(try( temp <-density(data.i$m.z)))
dens.mzA0 <- dens.mzA[dens.mzA !=0]
nofa <- max(medwin(as.numeric(names(dens.mzA0)),dens.mzA0/max(dens.mzA0))$y)
densityRescale <- T
if(!densityRescale){
nofa <- 1
}
temp$y <- temp$y/max(temp$y)*nofa
if(dens.crt == "try-error"){temp <- list(x=0,y=0)}
#
par(mai=c(0,0,0.1,0.1))
plotData$mz <- cbind(temp$x,temp$y)
plot(temp$y,temp$x,type = "n",axes = F,frame = F,ylim = range(c(data.i$m.z),na.rm = T),xlim = c(0,1),xlab = "Density",ylab = "",lwd = 1,col = "white")
# grid(col = "darkgrey",lwd = 1.5)
abline(h = pretty(temp$y),col = "darkgrey",lwd = 1.5,lty = "dotted")
quantiles <- quantile(data.i$m.z,na.rm =T)
#abline(h= quantiles[c(2,4)],col = IntQuanDensCol,lty = c("dashed","solid"),lwd = 1)
#points(temp$y,temp$x,type = "l",axes = F,frame = F,ylim = range(data.i$m.z,na.rm = T),xlab = "Density",ylab = "",lwd = 1,col = "grey30")
polygon(temp$y,temp$x,col = AllDensCol,border = AllDensCol)
Inner <- temp$x <= quantiles[4] & temp$x >= quantiles[2]
pX <- temp$x[Inner]
pY <- temp$y[Inner]
try(polygon(c(0,pY,0),c(min(pX),pX,max(pX)),col = IntQuanDensCol,border = IntQuanDensCol))
abline(h=median(data.i$m.z),col = "white",lwd = 2)
#axis(1,xpd = NA,las = 2)
#mtext("Density",1,line = 4,cex = 0.6)
if(BSACheck){
dens.crt <- class(try( temp <-density(data.i$m.z[BSAgrep])))
if(dens.crt == "try-error"){temp <- list(x=0,y=0)}
# par(mai=c(0,0,0.1,0.1))
# try( points(temp$y*BSAdensFactor,temp$x,type = "l",frame = F,ylim = range(data.i$m.z,na.rm = T),xlab = "Density",ylab = "",col = "white",lwd = 4))
# try( points(temp$y*BSAdensFactor,temp$x,type = "l",frame = F,ylim = range(data.i$m.z,na.rm = T),xlab = "Density",ylab = "",col = "#fca502",lwd = 3))
# try(legend("topright",legend = c("all","BSA"),col = c(AllDensCol,"#fca502"),bg = c(AllDensCol,"#fca502"),pch = 17,bty = "n",cex = 0.5))
}else{
# try(legend("topright",legend = c("all","con-\ntami-\nnants"),col = c(AllDensCol,"#fca502"),bg = c(AllDensCol,"#fca502"),pch = 17,bty = "n",cex = 0.5))
}
if(log2(ConFAC) > -4){
# try(points(tempCON$x,tempCON$y,type = "l",col = "#fca502",lwd = 2,lty = "dotted"))
try(plotPOL(a <- unfactor(dens.mzCA/max(c(dens.mzA,dens.mzCA))),b <- as.numeric(names(dens.mzCA)),col = "#fca50280",type = "p",border = "transparent"))
# points(dens.mzA/max(c(dens.mzA,dens.mzCA)),as.numeric(names(dens.mzA)),col = "#99999990",type = "h",border = "transparent")
#points(tempCON$x,tempCON$y,main = "",axes = F,frame = F,na.rm = T,type = "l",xlab = "",ylab = "Density",col = "dark#fca502",lwd = 3)
# try(legend("topright",legend = c("contaminants"),col = c("grey"),lty = "dotted",lwd = 3,bty = "n"))
}
try(plotPOL(a <- unfactor(dens.mzA/max(c(dens.mzA,dens.mzCA))),b <- as.numeric(names(dens.mzA)),col = "#99999990",type = "p",border = "transparent"))
# axis(2,xpd = NA,labels = F,padj = 0.5,tck = 0.04)
par(mai = c(0,0,0,0))
plot(1,type = "n",frame = F,axes = F)
if(BSACheck){
# try( points(temp$y*BSAdensFactor,temp$x,type = "l",frame = F,ylim = range(data.i$m.z,na.rm = T),xlab = "Density",ylab = "",col = "white",lwd = 4))
# try( points(temp$y*BSAdensFactor,temp$x,type = "l",frame = F,ylim = range(data.i$m.z,na.rm = T),xlab = "Density",ylab = "",col = "#fca502",lwd = 3))
try(legend("topleft",legend = c("other","BSA"),title = "Peptides",col = c(AllDensCol,"#fca502"),bg = c(AllDensCol,"#fca502"),pch = 17,bty = "n",cex = 0.5))
}else{
try(legend("topleft",legend = c("other","contaminants"),title = "Peptides",col = c(AllDensCol,"#fca502"),bg = c(AllDensCol,"#fca502"),pch = 17,bty = "n",cex = 0.5))
}
plotData$name.file <- name.file
if(length(funfun) > 0 & exists("msScans")){
par(mai=c(0.8,1,0,0))
try(funfun(msScans = msScans,msmsScans = msmsScans,xl = xl))
mtext("time in min",1,line = 1.9,cex = 0.6)
#axis(2,xpd = NA,las = 2)
axis(1)
abline(v= quantiles[c(2,4)],col = IntQuanDensCol,lty = c("dashed","solid"),lwd = 1)
}else{
mtext("time in min",1,line = 1.9,cex = 0.6)
#axis(2,xpd = NA,las = 2)
axis(1)
abline(v= quantiles[c(2,4)],col = IntQuanDensCol,lty = c("dashed","solid"),lwd = 1)
empty.plot()
}
print("Finished Plotting Scores")
}
return(plotData)
}
# sink(
# )
# sink()
# library(mqqc)
# graphics.off()
# pdf("test.pdf")
# path <- "/Users/henno/temp/mqqc/_RmqqcFile_Old/Test2/Beaker_20180219_OP_HSstd_Px08_HeLa_100ng_MQQCreanalyzedraw_folder - Copy/combined/txt/evidence.txt"
# temp <- read.csv(path,sep = "\t",stringsAsFactors = F)
# table(temp$raw.file)
# colnames(temp) <- tolower(colnames(temp))
# plot.profile(temp,linePlot = T,plot.legend = F,layout = F,addDensities = F)
# dev.off()
# system("open test.pdf")
# tryError2 <- class(try(TotalScoreRes <- plot.scores(data.i = temp.DataEvidence,msScans = msScans,msmsScans= msmsScans,data.list = qc.prepare.data,pdf.name = i, open.doc = open.doc,pdfOut = pdfOut, BSACheck = BSACheck)))
# tryError2 <- class(try(TotalScoreRes <- plot.scores(data.i = temp.DataEvidence,msScans = msScans,msmsScans= msmsScans,data.list = qc.prepare.data,pdf.name = i, open.doc = T,pdfOut = pdfOut, BSACheck = BSACheck)))
# plotMsFun <- NULL
# tryError2 <- class(try(TotalScoreRes <- plot.scores(data.i = temp.DataEvidence,msScans = NULL,msmsScans= NULL,data.list = qc.prepare.data,pdf.name = i, open.doc = T,pdfOut = pdfOut, BSACheck = BSACheck)))
# plot.profile(data.i,linePlot = T)
#try(plotData<- plot.profile(data.i,T,dots,BSACheck= BSACheck,plot.legend = F))
#plot.profile(temp.DataEvidence)
#tryError2 <- class(try(TotalScoreRes <- plot.scores(data.i = temp.DataEvidence,data.list = qc.prepare.data,pdf.name = i, open.doc = T,pdfOut = pdfOut, BSACheck = BSACheck)))
#par(mfrow = c(2,2))
#try(plotData<- plot.profile(data.i,F,F,BSACheck= T))
#plot.profile(Data)
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