Mercurial > repos > davidvanzessen > argalaxy_tools
comparison report_clonality/RScript.r @ 34:f2010de70741 draft
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| author | davidvanzessen |
|---|---|
| date | Mon, 18 Jan 2016 07:55:31 -0500 |
| parents | 672d5e010b1f |
| children | fd55088e48d2 |
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| 33:2d38d7c1d0d0 | 34:f2010de70741 |
|---|---|
| 482 DJList = split(completeDJ, f=completeDJ[,"Sample"]) | 482 DJList = split(completeDJ, f=completeDJ[,"Sample"]) |
| 483 lapply(DJList, FUN=plotDJ) | 483 lapply(DJList, FUN=plotDJ) |
| 484 } | 484 } |
| 485 | 485 |
| 486 | 486 |
| 487 # ---------------------- output tables for the circos plots ---------------------- | |
| 488 | |
| 489 print("Report Clonality - Circos data") | |
| 490 | |
| 491 for(smpl in unique(PRODF$Sample)){ | |
| 492 PRODF.sample = PRODF[PRODF$Sample == smpl,] | |
| 493 | |
| 494 fltr = PRODF.sample$Top.V.Gene == "" | |
| 495 if(sum(fltr) > 0){ | |
| 496 PRODF.sample[fltr, "Top.V.Gene"] = "NA" | |
| 497 } | |
| 498 | |
| 499 fltr = PRODF.sample$Top.D.Gene == "" | |
| 500 if(sum(fltr) > 0){ | |
| 501 PRODF.sample[fltr, "Top.D.Gene"] = "NA" | |
| 502 } | |
| 503 | |
| 504 fltr = PRODF.sample$Top.J.Gene == "" | |
| 505 if(sum(fltr) > 0){ | |
| 506 PRODF.sample[fltr, "Top.J.Gene"] = "NA" | |
| 507 } | |
| 508 | |
| 509 v.d = table(PRODF.sample$Top.V.Gene, PRODF.sample$Top.D.Gene) | |
| 510 v.j = table(PRODF.sample$Top.V.Gene, PRODF.sample$Top.J.Gene) | |
| 511 d.j = table(PRODF.sample$Top.D.Gene, PRODF.sample$Top.J.Gene) | |
| 512 | |
| 513 write.table(v.d, file=paste(smpl, "_VD_circos.txt", sep=""), sep="\t", quote=F, row.names=T, col.names=NA) | |
| 514 write.table(v.j, file=paste(smpl, "_VJ_circos.txt", sep=""), sep="\t", quote=F, row.names=T, col.names=NA) | |
| 515 write.table(d.j, file=paste(smpl, "_DJ_circos.txt", sep=""), sep="\t", quote=F, row.names=T, col.names=NA) | |
| 516 } | |
| 517 | |
| 487 # ---------------------- calculating the clonality score ---------------------- | 518 # ---------------------- calculating the clonality score ---------------------- |
| 488 | 519 |
| 489 if("Replicate" %in% colnames(inputdata)) #can only calculate clonality score when replicate information is available | 520 if("Replicate" %in% colnames(inputdata)) #can only calculate clonality score when replicate information is available |
| 490 { | 521 { |
| 522 print("Report Clonality - Clonality") | |
| 491 if(clonality_method == "boyd"){ | 523 if(clonality_method == "boyd"){ |
| 492 samples = split(clonalityFrame, clonalityFrame$Sample, drop=T) | 524 samples = split(clonalityFrame, clonalityFrame$Sample, drop=T) |
| 493 | 525 |
| 494 for (sample in samples){ | 526 for (sample in samples){ |
| 495 res = data.frame(paste=character(0)) | 527 res = data.frame(paste=character(0)) |