Mercurial > repos > davidvanzessen > plotting_merged

comparison RScript.r @ 51:8f5ab5290c88 draft

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author davidvanzessen
date Tue, 10 Dec 2013 07:21:31 -0500
parents 3da85f1a7f42
children 907e2a756f85
comparison
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50:e6209052aaf4 51:8f5ab5290c88
36 36
37 #test$VDJCDR3 = do.call(paste, c(test[c("Top.V.Gene", "Top.D.Gene", "Top.J.Gene","CDR3.Seq.DNA")], sep = ":")) 37 #test$VDJCDR3 = do.call(paste, c(test[c("Top.V.Gene", "Top.D.Gene", "Top.J.Gene","CDR3.Seq.DNA")], sep = ":"))
38 test$VDJCDR3 = do.call(paste, c(test[unlist(strsplit(clonalType, ","))], sep = ":")) 38 test$VDJCDR3 = do.call(paste, c(test[unlist(strsplit(clonalType, ","))], sep = ":"))
39 39
40 PROD = test[test$VDJ.Frame != "In-frame with stop codon" & test$VDJ.Frame != "Out-of-frame" & test$CDR3.Found.How != "NOT_FOUND" , ] 40 PROD = test[test$VDJ.Frame != "In-frame with stop codon" & test$VDJ.Frame != "Out-of-frame" & test$CDR3.Found.How != "NOT_FOUND" , ]
41 if("Functionality" %in% colnames(test)) {
42 PROD = test[test$Functionality == "productive" | test$Functionality == "productive (see comment)", ]
43 }
41 44
42 NONPROD = test[test$VDJ.Frame == "In-frame with stop codon" | test$VDJ.Frame == "Out-of-frame" | test$CDR3.Found.How == "NOT_FOUND" , ] 45 NONPROD = test[test$VDJ.Frame == "In-frame with stop codon" | test$VDJ.Frame == "Out-of-frame" | test$CDR3.Found.How == "NOT_FOUND" , ]
43 46
44 #PRODF = PROD[ -1] 47 #PRODF = PROD[ -1]
45 48
88 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)
89 close(tcJ) 92 close(tcJ)
90 93
91 setwd(outDir) 94 setwd(outDir)
92 95
93 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)
94 97
95 pV = ggplot(PRODFV) 98 pV = ggplot(PRODFV)
96 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))
97 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")
98 101
231 if("Replicate" %in% colnames(test)) 234 if("Replicate" %in% colnames(test))
232 { 235 {
233 clonalityFrame = PROD 236 clonalityFrame = PROD
234 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 = ":"))
235 clonalityFrame = clonalityFrame[!duplicated(clonalityFrame$ReplicateConcat), ] 238 clonalityFrame = clonalityFrame[!duplicated(clonalityFrame$ReplicateConcat), ]
236 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)
237 240
238 ClonalitySampleReplicatePrint <- function(dat){ 241 ClonalitySampleReplicatePrint <- function(dat){
239 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)
240 } 243 }
241 244
242 clonalityFrameSplit = split(clonalityFrame, f=clonalityFrame[,c("Sample", "Replicate")]) 245 clonalityFrameSplit = split(clonalityFrame, f=clonalityFrame[,c("Sample", "Replicate")])
243 lapply(clonalityFrameSplit, FUN=ClonalitySampleReplicatePrint) 246 lapply(clonalityFrameSplit, FUN=ClonalitySampleReplicatePrint)
244 247
245 ClonalitySamplePrint <- function(dat){ 248 ClonalitySamplePrint <- function(dat){
246 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)
247 } 250 }
248 251
249 clonalityFrameSplit = split(clonalityFrame, f=clonalityFrame[,"Sample"]) 252 clonalityFrameSplit = split(clonalityFrame, f=clonalityFrame[,"Sample"])
250 lapply(clonalityFrameSplit, FUN=ClonalitySamplePrint) 253 lapply(clonalityFrameSplit, FUN=ClonalitySamplePrint)
251 254