comparison RScript.r @ 51:8f5ab5290c88 draft

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50:e6209052aaf4

#test$VDJCDR3 = do.call(paste, c(test[c("Top.V.Gene", "Top.D.Gene", "Top.J.Gene","CDR3.Seq.DNA")], sep = ":"))
test$VDJCDR3 = do.call(paste, c(test[unlist(strsplit(clonalType, ","))], sep = ":"))

PROD = test[test$VDJ.Frame != "In-frame with stop codon" & test$VDJ.Frame != "Out-of-frame" & test$CDR3.Found.How != "NOT_FOUND" , ]

NONPROD = test[test$VDJ.Frame == "In-frame with stop codon" | test$VDJ.Frame == "Out-of-frame" | test$CDR3.Found.How == "NOT_FOUND" , ]

#PRODF = PROD[ -1]

PRODFJ = merge(PRODFJ, Jchain, by.x='Top.J.Gene', by.y='v.name', all.x=TRUE)
close(tcJ)

setwd(outDir)

write.table(PRODF, "allUnique.tsv", sep="\t",quote=F,row.names=T,col.names=T)

pV = ggplot(PRODFV)
pV = pV + geom_bar( aes( x=factor(reorder(Top.V.Gene, chr.orderV)), y=relFreq, fill=Sample), stat='identity', position="dodge") + theme(axis.text.x = element_text(angle = 90, hjust = 1))
pV = pV + xlab("Summary of V gene") + ylab("Frequency") + ggtitle("Relative frequency of V gene usage")

if("Replicate" %in% colnames(test))
{
	clonalityFrame = PROD
	clonalityFrame$ReplicateConcat = do.call(paste, c(clonalityFrame[c("VDJCDR3", "Sample", "Replicate")], sep = ":"))
	clonalityFrame = clonalityFrame[!duplicated(clonalityFrame$ReplicateConcat), ]
	write.table(clonalityFrame, "clonalityComplete.tsv", sep="\t",quote=F,row.names=T,col.names=T)

	ClonalitySampleReplicatePrint <- function(dat){
	    write.table(dat, paste("clonality_", unique(dat$Sample) , "_", unique(dat$Replicate), ".tsv", sep=""), sep="\t",quote=F,row.names=T,col.names=T)
	}

    clonalityFrameSplit = split(clonalityFrame, f=clonalityFrame[,c("Sample", "Replicate")])
    lapply(clonalityFrameSplit, FUN=ClonalitySampleReplicatePrint)

    ClonalitySamplePrint <- function(dat){
	    write.table(dat, paste("clonality_", unique(dat$Sample) , ".tsv", sep=""), sep="\t",quote=F,row.names=T,col.names=T)
	}

    clonalityFrameSplit = split(clonalityFrame, f=clonalityFrame[,"Sample"])
    lapply(clonalityFrameSplit, FUN=ClonalitySamplePrint)

51:8f5ab5290c88

#test$VDJCDR3 = do.call(paste, c(test[c("Top.V.Gene", "Top.D.Gene", "Top.J.Gene","CDR3.Seq.DNA")], sep = ":"))
test$VDJCDR3 = do.call(paste, c(test[unlist(strsplit(clonalType, ","))], sep = ":"))

PROD = test[test$VDJ.Frame != "In-frame with stop codon" & test$VDJ.Frame != "Out-of-frame" & test$CDR3.Found.How != "NOT_FOUND" , ]
if("Functionality" %in% colnames(test)) {
	PROD = test[test$Functionality == "productive" | test$Functionality == "productive (see comment)", ]
}

NONPROD = test[test$VDJ.Frame == "In-frame with stop codon" | test$VDJ.Frame == "Out-of-frame" | test$CDR3.Found.How == "NOT_FOUND" , ]

#PRODF = PROD[ -1]

PRODFJ = merge(PRODFJ, Jchain, by.x='Top.J.Gene', by.y='v.name', all.x=TRUE)
close(tcJ)

setwd(outDir)

write.table(PRODF, "allUnique.tsv", sep="\t",quote=F,row.names=F,col.names=T)

pV = ggplot(PRODFV)
pV = pV + geom_bar( aes( x=factor(reorder(Top.V.Gene, chr.orderV)), y=relFreq, fill=Sample), stat='identity', position="dodge") + theme(axis.text.x = element_text(angle = 90, hjust = 1))
pV = pV + xlab("Summary of V gene") + ylab("Frequency") + ggtitle("Relative frequency of V gene usage")

if("Replicate" %in% colnames(test))
{
	clonalityFrame = PROD
	clonalityFrame$ReplicateConcat = do.call(paste, c(clonalityFrame[c("VDJCDR3", "Sample", "Replicate")], sep = ":"))
	clonalityFrame = clonalityFrame[!duplicated(clonalityFrame$ReplicateConcat), ]
	write.table(clonalityFrame, "clonalityComplete.tsv", sep="\t",quote=F,row.names=F,col.names=T)

	ClonalitySampleReplicatePrint <- function(dat){
	    write.table(dat, paste("clonality_", unique(dat$Sample) , "_", unique(dat$Replicate), ".tsv", sep=""), sep="\t",quote=F,row.names=F,col.names=T)
	}

    clonalityFrameSplit = split(clonalityFrame, f=clonalityFrame[,c("Sample", "Replicate")])
    lapply(clonalityFrameSplit, FUN=ClonalitySampleReplicatePrint)

    ClonalitySamplePrint <- function(dat){
	    write.table(dat, paste("clonality_", unique(dat$Sample) , ".tsv", sep=""), sep="\t",quote=F,row.names=F,col.names=T)
	}

    clonalityFrameSplit = split(clonalityFrame, f=clonalityFrame[,"Sample"])
    lapply(clonalityFrameSplit, FUN=ClonalitySamplePrint)