R/msmsPlot.R

In mqqc: Quality control of LCMS derived proteomic data

msmsPlot <- 
function(pdfOut = T,path = "./", RawFilesUsed = NULL, quant.range = NULL,MSMS.Import= NULL){
msmsPath <- list.files(path, pattern="msms.txt",full.name = T)
if(length(msmsPath) > 0){
	

	if(length(MSMS.Import)== 0){
	MSMS.Import <- read.table(msmsPath,colClasses = "character",sep = "\t",comment.char = "",header = T)
  # using raw.file intensities
	}
	Header <- colnames(MSMS.Import)
	colnames(MSMS.Import) <- tolower(make.names(colnames(MSMS.Import)))
	#colnames(MSMS.Import) <- tolower(make.names(MSMS.Import[1,]))
	#	MSMS.Import <- MSMS.Import[-1,]

	if(length(RawFilesUsed) > 0){
		mergeTemp <- merge.control(MSMS.Import$raw.file,RawFilesUsed)
		mergeTemp  <- mergeTemp[!is.na(mergeTemp)] 
		if(length(mergeTemp) > 0){
			MSMS.Import <- MSMS.Import[unique(mergeTemp),]
		}
	}
	if(length(unique(MSMS.Import$raw.file))== 1){
		
		.name 	<- paste("MSMS_Dens",unique(MSMS.Import$raw.file),sep = "_")
		.name 	<- gsub(".raw$","",.name)
		.name <- paste(.name,".pdf",sep = "")
	}else{
		.name <- "MSMS_Dis.pdf"
	}
	# Checking MSMS ID in quantrange:
	if(length(quant.range) > 0){
		#Hu <- subset(MSMS.Import,select = "")
	}
	
	
	# 	if(pdfOut){
	# 	pdf(.name,pointsize = 20,width = 10)
	# par(mai = c(1.5,1.5,0.3,0.2))
	# }
	

	 test <<- quantile(temp <- as.numeric(unlist(strsplit(as.character(MSMS.Import$intensities),";"))),na.rm  =T)
	 MSMS.N <- sapply( strsplit(as.character(MSMS.Import$intensities),";"),length)
	 MSMS.N <- quantile(MSMS.N[MSMS.N != 0])

# huha <-temp/MSMS.N
# huha <- huha[!is.infinite(huha)]
# huha <- huha[huha !=0]
# test <- quantile(huha)
	 
	 
	 #hist(log10(temp),breaks = 100)
windows = 5
MinuteWindow <- ceiling(max(as.numeric(MSMS.Import$retention.time)) /windows)
init = as.numeric(MSMS.Import$retention.time)
for(i in windows:1){
	init[as.numeric(MSMS.Import$retention.time) <= MinuteWindow*i ] <- as.character(paste((i-1)*MinuteWindow,"to",i*MinuteWindow,"min"))
}


legInfo <- aggregate(MSMS.Import$intensities,list(init),function(x){

	temp <- as.numeric(unlist(strsplit(as.character(x),";")))
	
	return(temp)
})
Data  					<- legInfo[2]
rownames(Data) 	<- sapply(legInfo[1],as.character)
Data <- apply(Data,1,unlist)
DataL <- unlist(lapply(Data,length))

Data2 <- Data[order(DataL,decreasing = T)]	
# DataL <- DataL[order(DataL)]
# cols <- rainbow(length(Data2)+1, alpha = 1,start = 0.1, end = 1,s = 0.9,v = 0.9)
# a <- 1
# maxv <- 0
# maxx <- 2
# orderMax <- c()
# #Data2$all <-  as.numeric(unlist(strsplit(as.character(MSMS.Import$intensities),";")))
# # DataL <- c(DataL,length(Data2$all))
# #names(DataL)[length(DataL)] <- "all"
# 
# 
# colsVec <- lapply(Data2,function(x){
# 	if(length(x) == 1){
# 		x <- c(x,x)
# 	}
# 	if(length(x)> 1){
# 	dens <- density(as.numeric(log10(x)),na.rm = T)
# 	maxv <<- max(maxv,max(dens$y),na.rm = T)
# 	maxx <<- c(min(maxx,min(dens$x),na.rm = T),max(maxx,max(dens$x),na.rm = T))
# 	orderMax <<- c(orderMax,max(dens$y,na.rm = T))
# 	}else{
# 		dens <- list(x = c(0,0),y = c(0,0))
# 	}
# 	return(dens)
# })
# 
# maxx <- maxx+ maxx*c(0,0.2)
# 
# plot(1,type = "n",ylim = c(0, maxv),ylab = "Density",xlab = "log10(Intensity)",frame = F,xlim = maxx,main = "Fragment Ions Density Plot",sub = .name,mgp = c(2.3,1,0))
# grid(lwd = 4)
# a <- 1
# colsVec 	<- colsVec[order(orderMax,decreasing = T)]
# cols 		<- cols[order(orderMax,decreasing = T)]
# DataL 		<- DataL[merge.control(names(DataL),names(colsVec))]
# DataRel 	<- DataL/max(DataL)
# lapply(colsVec,function(x){
# 		
# 	x$y <- x$y * DataRel[a]
# 	points(x,col = "white",type = "l",lwd = 7)
# 	points(x,col = cols[a],type = "l",lwd = 4)
# 	
# 	a <<- a+1
# })
# 
# legend("topright",legend = paste(names(colsVec),"n:",DataL[merge.control(names(DataL),names(colsVec))])[order(names(colsVec))],col = cols[order(names(colsVec))],lwd = 10,bty = "n",cex = 1,xpd = NA, xjust = 0.5,title = paste(MinuteWindow,"min windows"))
# 
# if(pdfOut){
# graphics.off()	
# }
return(list(MSMSint = quantile(unlist(Data2),na.rm = T),MSMSn = quantile(MSMS.N[MSMS.N != 0],na.rm = T)))

}else{return(rep(0,5))}
}


#try(msmsInfo <- msmsPlot(path = path, RawFilesUsed=  RawFilesUsed))
#hz.show.path(getwd())
#msmsPlot(.path,pdfOut = T)