diff RScript.r @ 0:c5ac9a871b26 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/RScript.r	Thu Jun 19 10:39:41 2014 -0400
@@ -0,0 +1,173 @@
+args <- commandArgs(trailingOnly = TRUE)
+
+inFile = args[1]
+outDir = args[2]
+
+require(ggplot2)
+require(reshape2)
+require(data.table)
+require(grid)
+#require(xtable)
+#dat = read.csv(inFile)
+dat = data.frame(fread(inFile)) #faster but with a dep
+setwd(outDir)
+dat$Frequency = ((10^dat$Log10_Frequency)*100)
+patients = split(dat, dat$Patient, drop=T)
+intervalReads = rev(c(0,2,10,100,1000,10000))
+intervalFreq = rev(c(0,0.01,0.1,0.5,1,5))
+V_Segments = c(".*", "IGHV", "IGHD", "IGKV", "IGKV", "IgKINTR", "TRGV", "TRDV", "TRDD" , "TRBV")
+J_Segments = c(".*", ".*", ".*", "IGKJ", "KDE", ".*", ".*", ".*", ".*", ".*")
+Titles = c("Total", "IGH-Vh-Jh", "IGH-Dh-Jh", "Vk-Jk", "Vk-Kde" , "Intron-Kde", "TCRG", "TCRD-Vd-Dd", "TCRD-Dd-Dd", "TCRB-Vb-Jb")
+Titles = factor(Titles, levels=Titles)
+TitlesOrder = data.frame("Title"=Titles, "TitlesOrder"=1:length(Titles))
+
+patientCountOnColumn <- function(x, product, interval, on, appendtxt=F){
+  x$Sample = factor(x$Sample, levels=unique(x$Sample))
+  onShort = "reads"
+  if(on == "Frequency"){
+    onShort = "freq"
+  }
+  splt = split(x, x$Sample, drop=T)
+  patient1 = splt[[1]]
+  patient2 = splt[[2]]
+  
+  threshholdIndex = which(colnames(product) == "interval")
+  V_SegmentIndex = which(colnames(product) == "V_Segments")
+  J_SegmentIndex = which(colnames(product) == "J_Segments")
+  titleIndex = which(colnames(product) == "Titles")
+  sampleIndex = which(colnames(x) == "Sample")
+  patientIndex = which(colnames(x) == "Patient")
+  oneSample = paste(patient1[1,sampleIndex], sep="")
+  twoSample = paste(patient2[1,sampleIndex], sep="")
+  patient = paste(x[1,patientIndex])
+  
+  #print(c(length(grep(".*_Right$", twoSample)) == 1, "Right"))
+  #print(c(length(grep(".*_Dx_BM$", twoSample)) == 1, "Dx_BM"))
+  #print(c(length(grep(".*_Dx$", twoSample)) == 1, "Dx"))
+  switched = F
+  if(length(grep(".*_Right$", twoSample)) == 1 || length(grep(".*_Dx_BM$", twoSample)) == 1 || length(grep(".*_Dx$", twoSample)) == 1 ){
+    tmp = twoSample
+    twoSample = oneSample
+    oneSample = tmp
+    tmp = patient1
+    patient1 = patient2
+    patient2 = tmp
+    switched = T
+  }
+  if(appendtxt){
+    cat(paste(patient, oneSample, twoSample, sep="\t"), file="patients.txt", append=T, sep="", fill=3)
+  }
+  patientMerge = merge(patient1, patient2, by="Clone_Sequence")
+  res1 = vector()
+  res2 = vector()
+  resBoth = vector()
+  read1Count = vector()
+  read2Count = vector()
+  
+  print(c(patient, " ", on))
+  #for(iter in 1){
+  for(iter in 1:length(product[,1])){
+    threshhold = product[iter,threshholdIndex]
+    V_Segment = paste(".*", as.character(product[iter,V_SegmentIndex]), ".*", sep="")
+    J_Segment = paste(".*", as.character(product[iter,J_SegmentIndex]), ".*", sep="")
+    both = (grepl(V_Segment, patientMerge$V_Segment_Major_Gene.x) & grepl(J_Segment, patientMerge$J_Segment_Major_Gene.x) & patientMerge[,paste(on, ".x", sep="")] > threshhold & patientMerge[,paste(on, ".y", sep="")] > threshhold)
+    one = (grepl(V_Segment, patient1$V_Segment_Major_Gene) & grepl(J_Segment, patient1$J_Segment_Major_Gene) & patient1[,on] > threshhold & !(patient1$Clone_Sequence %in% patientMerge[both,]$Clone_Sequence))
+    two = (grepl(V_Segment, patient2$V_Segment_Major_Gene) & grepl(J_Segment, patient2$J_Segment_Major_Gene) & patient2[,on] > threshhold & !(patient2$Clone_Sequence %in% patientMerge[both,]$Clone_Sequence))
+    read1Count = append(read1Count, sum(patient1[one,]$Clone_Molecule_Count_From_Spikes) + sum(patientMerge[both,]$Clone_Molecule_Count_From_Spikes.x))
+    read2Count = append(read2Count, sum(patient2[two,]$Clone_Molecule_Count_From_Spikes) + sum(patientMerge[both,]$Clone_Molecule_Count_From_Spikes.y))
+    res1 = append(res1, sum(one))
+    res2= append(res2, sum(two))
+    resBoth = append(resBoth, sum(both))
+    #threshhold = 0
+    if(threshhold != 0){
+      if(sum(one) > 0){
+        dfOne = patient1[one,c("V_Segment_Major_Gene", "J_Segment_Major_Gene", "Clone_Molecule_Count_From_Spikes", "Frequency", "Clone_Sequence")]
+        colnames(dfOne) = c("Proximal segment", "Distal segment", "Clone_Molecule_Count_From_Spikes", "Frequency", "Sequence")
+        filenameOne = paste(oneSample, "_", product[iter, titleIndex], "_", threshhold, sep="")
+        #print(xtable(dfOne),type="html", file=paste(filenameOne, ".html", sep=""), include.rownames=FALSE)
+        write.table(dfOne, file=paste(filenameOne, ".txt", sep=""), quote=F, sep="\t", dec=",", row.names=F, col.names=T)
+      }
+      if(sum(two) > 0){
+        dfTwo = patient2[two,c("V_Segment_Major_Gene", "J_Segment_Major_Gene", "Clone_Molecule_Count_From_Spikes", "Frequency", "Clone_Sequence")]
+        colnames(dfTwo) = c("Proximal segment", "Distal segment", "Clone_Molecule_Count_From_Spikes", "Frequency", "Sequence")
+        filenameTwo = paste(twoSample, "_", product[iter, titleIndex], "_", threshhold, sep="")
+        #print(xtable(dfTwo),type="html", file=paste(filenameTwo, ".html", sep=""), include.rownames=FALSE)
+        write.table(dfTwo, file=paste(filenameTwo, ".txt", sep=""), quote=F, sep="\t", dec=",", row.names=F, col.names=T)
+      }
+    }
+    if(sum(both) > 0){
+      dfBoth = patientMerge[both,c("V_Segment_Major_Gene.x", "J_Segment_Major_Gene.x", "Clone_Molecule_Count_From_Spikes.x", "Frequency.x", "Clone_Sequence", "V_Segment_Major_Gene.y", "J_Segment_Major_Gene.y", "Clone_Molecule_Count_From_Spikes.y", "Frequency.y")]
+      colnames(dfBoth) = c(paste("Proximal segment", oneSample), paste("Distal segment", oneSample), paste("Read Count", oneSample), paste("Frequency", oneSample), "Sequence", paste("Proximal segment", twoSample), paste("Distal segment", twoSample), paste("Read_Count", twoSample), paste("Frequency", twoSample))
+      filenameBoth = paste(oneSample, "_", twoSample, "_", product[iter, titleIndex], "_", threshhold, sep="")
+      #print(xtable(dfBoth),type="html", file=paste(filenameBoth, ".html", sep=""), include.rownames=FALSE)
+      write.table(dfBoth, file=paste(filenameBoth, ".txt", sep=""), quote=F, sep="\t", dec=",", row.names=F, col.names=T)
+    }
+  }
+  patientResult = data.frame("Locus"=product$Titles, "J_Segment"=product$J_Segments, "V_Segment"=product$V_Segments, "cut_off_value"=paste(">", product$interval, sep=""), "Both"=resBoth, "tmp1"=res1, "read_count1" = round(read1Count), "tmp2"=res2, "read_count2"= round(read2Count), "Sum"=res1 + res2 + resBoth, "percentage" = round((resBoth/(res1 + res2 + resBoth)) * 100, digits=2))
+  if(sum(is.na(patientResult$percentage)) > 0){
+    patientResult[is.na(patientResult$percentage),]$percentage = 0
+  }
+  colnames(patientResult)[6] = oneSample
+  colnames(patientResult)[8] = twoSample
+  colnamesBak = colnames(patientResult)
+  colnames(patientResult) = c("Ig/TCR gene rearrangement type", "Distal Gene segment", "Proximal gene segment", "cut_off_value", paste("Number of sequences ", patient, "_Both", sep=""), paste("Number of sequences", oneSample, sep=""), paste("Read Count", oneSample), paste("Number of sequences", twoSample, sep=""), paste("Read Count", twoSample), paste("Sum number of sequences", patient), paste("Percentage of sequences ", patient, "_Both", sep=""))
+  write.table(patientResult, file=paste(patient, "_", onShort, ".txt", sep=""), quote=F, sep="\t", dec=",", row.names=F, col.names=T)
+  colnames(patientResult) = colnamesBak
+  
+  patientResult$Locus = factor(patientResult$Locus, Titles)
+  patientResult$cut_off_value = factor(patientResult$cut_off_value, paste(">", interval, sep=""))
+  
+  plt = ggplot(patientResult[,c("Locus", "cut_off_value", "Both")])
+  plt = plt + geom_bar( aes( x=factor(cut_off_value), y=Both), stat='identity', position="dodge", fill="#79c36a")
+  plt = plt + facet_grid(.~Locus) + theme(axis.text.x = element_text(angle = 45, hjust = 1))
+  plt = plt + geom_text(aes(ymax=max(Both), x=cut_off_value,y=Both,label=Both), angle=90, hjust=0)
+  plt = plt + xlab("Reads per locus") + ylab("Count") + ggtitle("Number of clones in both")
+  plt = plt + theme(plot.margin = unit(c(1,8.8,0.5,1.5), "lines"))
+  png(paste(patient, "_", onShort, ".png", sep=""), width=1920, height=1080)
+  print(plt)
+  dev.off()
+  #(t,r,b,l)
+  plt = ggplot(patientResult[,c("Locus", "cut_off_value", "percentage")])
+  plt = plt + geom_bar( aes( x=factor(cut_off_value), y=percentage), stat='identity', position="dodge", fill="#79c36a")
+  plt = plt + facet_grid(.~Locus) + theme(axis.text.x = element_text(angle = 45, hjust = 1))
+  plt = plt + geom_text(aes(ymax=max(percentage), x=cut_off_value,y=percentage,label=percentage), angle=90, hjust=0)
+  plt = plt + xlab("Reads per locus") + ylab("Count") + ggtitle("% clones in both left and right")
+  plt = plt + theme(plot.margin = unit(c(1,8.8,0.5,1.5), "lines"))
+  png(paste(patient, "_percent_", onShort, ".png", sep=""), width=1920, height=1080)
+  print(plt)
+  dev.off()
+  
+  patientResult = melt(patientResult[,c('Locus','cut_off_value', oneSample, twoSample)] ,id.vars=1:2)
+  patientResult$relativeValue = patientResult$value * 10
+  patientResult[patientResult$relativeValue == 0,]$relativeValue = 1
+  plt = ggplot(patientResult)
+  plt = plt + geom_bar( aes( x=factor(cut_off_value), y=relativeValue, fill=variable), stat='identity', position="dodge")
+  plt = plt + facet_grid(.~Locus) + theme(axis.text.x = element_text(angle = 45, hjust = 1))
+  plt = plt + scale_y_continuous(trans="log", breaks=10^c(0:10), labels=c(0, 10^c(0:9)))
+  plt = plt + geom_text(data=patientResult[patientResult$variable == oneSample,], aes(ymax=max(value), x=cut_off_value,y=relativeValue,label=value), angle=90, position=position_dodge(width=0.9), hjust=0, vjust=-0.2)
+  plt = plt + geom_text(data=patientResult[patientResult$variable == twoSample,], aes(ymax=max(value), x=cut_off_value,y=relativeValue,label=value), angle=90, position=position_dodge(width=0.9), hjust=0, vjust=0.8)
+  plt = plt + xlab("Reads per locus") + ylab("Count") + ggtitle(paste("Number of clones in only ", oneSample, " and only ", twoSample, sep=""))
+  png(paste(patient, "_", onShort, "_both.png", sep=""), width=1920, height=1080)
+  print(plt)
+  dev.off()
+}
+
+interval = intervalFreq
+intervalOrder = data.frame("interval"=paste(">", interval, sep=""), "intervalOrder"=1:length(interval))
+product = data.frame("Titles"=rep(Titles, each=6), "interval"=rep(interval, times=10), "V_Segments"=rep(V_Segments, each=6), "J_Segments"=rep(J_Segments, each=6))
+#patientFrequencyCount(patient1)
+#lapply(patients[c(5,6,10)], FUN=patientFrequencyCount)
+#lapply(patients[c(5,6,7,8,13)], FUN=patientCountOnColumn, product = product, interval=interval, on="Frequency", appendtxt=T)
+#lapply(patients[c(6,7,8)], FUN=patientCountOnColumn, product = product, interval=interval, on="Frequency", appendtxt=T)
+#lapply(patients[c(6)], FUN=patientCountOnColumn, product = product, interval=interval, on="Frequency", appendtxt=T)
+lapply(patients, FUN=patientCountOnColumn, product = product, interval=interval, on="Frequency", appendtxt=T)
+
+interval = intervalReads
+intervalOrder = data.frame("interval"=paste(">", interval, sep=""), "intervalOrder"=1:length(interval))
+product = data.frame("Titles"=rep(Titles, each=6), "interval"=rep(interval, times=10), "V_Segments"=rep(V_Segments, each=6), "J_Segments"=rep(J_Segments, each=6))
+#patientResult = patientReadCount(patient1)
+#lapply(patients[c(5,6,10)], FUN=patientReadCount)
+#lapply(patients[c(5,6,7,8,13)], FUN=patientCountOnColumn, product = product, interval=interval, on="Clone_Molecule_Count_From_Spikes")
+#lapply(patients[c(6)], FUN=patientCountOnColumn, product = product, interval=interval, on="Clone_Molecule_Count_From_Spikes")
+lapply(patients, FUN=patientCountOnColumn, product = product, interval=interval, on="Clone_Molecule_Count_From_Spikes")
+