Mercurial > repos > davidvanzessen > combined_immune_repertoire_pipeline

comparison RScript.r @ 10:a5c224bb0be5 draft

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author davidvanzessen
date Tue, 10 Dec 2013 07:22:56 -0500
parents 8d83319a0f3d
children a15d060a6248
comparison
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9:8d83319a0f3d 10:a5c224bb0be5
91 PRODFJ = merge(PRODFJ, Jchain, by.x='Top.J.Gene', by.y='v.name', all.x=TRUE) 91 PRODFJ = merge(PRODFJ, Jchain, by.x='Top.J.Gene', by.y='v.name', all.x=TRUE)
92 close(tcJ) 92 close(tcJ)
93 93
94 setwd(outDir) 94 setwd(outDir)
95 95
96 write.table(PRODF, "allUnique.tsv", sep="\t",quote=F,row.names=T,col.names=T) 96 write.table(PRODF, "allUnique.tsv", sep="\t",quote=F,row.names=F,col.names=T)
97 97
98 pV = ggplot(PRODFV) 98 pV = ggplot(PRODFV)
99 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)) 99 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))
100 pV = pV + xlab("Summary of V gene") + ylab("Frequency") + ggtitle("Relative frequency of V gene usage") 100 pV = pV + xlab("Summary of V gene") + ylab("Frequency") + ggtitle("Relative frequency of V gene usage")
101 101
234 if("Replicate" %in% colnames(test)) 234 if("Replicate" %in% colnames(test))
235 { 235 {
236 clonalityFrame = PROD 236 clonalityFrame = PROD
237 clonalityFrame$ReplicateConcat = do.call(paste, c(clonalityFrame[c("VDJCDR3", "Sample", "Replicate")], sep = ":")) 237 clonalityFrame$ReplicateConcat = do.call(paste, c(clonalityFrame[c("VDJCDR3", "Sample", "Replicate")], sep = ":"))
238 clonalityFrame = clonalityFrame[!duplicated(clonalityFrame$ReplicateConcat), ] 238 clonalityFrame = clonalityFrame[!duplicated(clonalityFrame$ReplicateConcat), ]
239 write.table(clonalityFrame, "clonalityComplete.tsv", sep="\t",quote=F,row.names=T,col.names=T) 239 write.table(clonalityFrame, "clonalityComplete.tsv", sep="\t",quote=F,row.names=F,col.names=T)
240 240
241 ClonalitySampleReplicatePrint <- function(dat){ 241 ClonalitySampleReplicatePrint <- function(dat){
242 write.table(dat, paste("clonality_", unique(dat$Sample) , "_", unique(dat$Replicate), ".tsv", sep=""), sep="\t",quote=F,row.names=T,col.names=T) 242 write.table(dat, paste("clonality_", unique(dat$Sample) , "_", unique(dat$Replicate), ".tsv", sep=""), sep="\t",quote=F,row.names=F,col.names=T)
243 } 243 }
244 244
245 clonalityFrameSplit = split(clonalityFrame, f=clonalityFrame[,c("Sample", "Replicate")]) 245 clonalityFrameSplit = split(clonalityFrame, f=clonalityFrame[,c("Sample", "Replicate")])
246 lapply(clonalityFrameSplit, FUN=ClonalitySampleReplicatePrint) 246 lapply(clonalityFrameSplit, FUN=ClonalitySampleReplicatePrint)
247 247
248 ClonalitySamplePrint <- function(dat){ 248 ClonalitySamplePrint <- function(dat){
249 write.table(dat, paste("clonality_", unique(dat$Sample) , ".tsv", sep=""), sep="\t",quote=F,row.names=T,col.names=T) 249 write.table(dat, paste("clonality_", unique(dat$Sample) , ".tsv", sep=""), sep="\t",quote=F,row.names=F,col.names=T)
250 } 250 }
251 251
252 clonalityFrameSplit = split(clonalityFrame, f=clonalityFrame[,"Sample"]) 252 clonalityFrameSplit = split(clonalityFrame, f=clonalityFrame[,"Sample"])
253 lapply(clonalityFrameSplit, FUN=ClonalitySamplePrint) 253 lapply(clonalityFrameSplit, FUN=ClonalitySamplePrint)
254 254