Mercurial > repos > davidvanzessen > argalaxy_tools

comparison report_clonality/RScript.r @ 52:371c568408e9 draft

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author davidvanzessen
date Fri, 29 Jan 2016 05:29:52 -0500
parents 2a79f9adf89b
children 379856bef228
comparison
equal deleted inserted replaced
51:d3d4823c101a 52:371c568408e9
454 cartegianProductVD = expand.grid(Top.V.Gene = Vchain$v.name, Top.D.Gene = Dchain$v.name, Sample = unique(inputdata$Sample)) 454 cartegianProductVD = expand.grid(Top.V.Gene = Vchain$v.name, Top.D.Gene = Dchain$v.name, Sample = unique(inputdata$Sample))
455 455
456 completeVD = merge(VandDCount, cartegianProductVD, all.y=TRUE) 456 completeVD = merge(VandDCount, cartegianProductVD, all.y=TRUE)
457 completeVD = merge(completeVD, revVchain, by.x="Top.V.Gene", by.y="v.name", all.x=TRUE) 457 completeVD = merge(completeVD, revVchain, by.x="Top.V.Gene", by.y="v.name", all.x=TRUE)
458 completeVD = merge(completeVD, Dchain, by.x="Top.D.Gene", by.y="v.name", all.x=TRUE) 458 completeVD = merge(completeVD, Dchain, by.x="Top.D.Gene", by.y="v.name", all.x=TRUE)
459
460 if(any(fltr, na.rm=T)){
461 completeVD[fltr,"relLength"] = 1
462 }
463
459 VDList = split(completeVD, f=completeVD[,"Sample"]) 464 VDList = split(completeVD, f=completeVD[,"Sample"])
460 lapply(VDList, FUN=plotVD) 465 lapply(VDList, FUN=plotVD)
461 } 466 }
462 467
463 print("Report Clonality - Heatmaps VJ") 468 print("Report Clonality - Heatmaps VJ")
491 cartegianProductVJ = expand.grid(Top.V.Gene = Vchain$v.name, Top.J.Gene = Jchain$v.name, Sample = unique(inputdata$Sample)) 496 cartegianProductVJ = expand.grid(Top.V.Gene = Vchain$v.name, Top.J.Gene = Jchain$v.name, Sample = unique(inputdata$Sample))
492 497
493 completeVJ = merge(VandJCount, cartegianProductVJ, all.y=TRUE) 498 completeVJ = merge(VandJCount, cartegianProductVJ, all.y=TRUE)
494 completeVJ = merge(completeVJ, revVchain, by.x="Top.V.Gene", by.y="v.name", all.x=TRUE) 499 completeVJ = merge(completeVJ, revVchain, by.x="Top.V.Gene", by.y="v.name", all.x=TRUE)
495 completeVJ = merge(completeVJ, Jchain, by.x="Top.J.Gene", by.y="v.name", all.x=TRUE) 500 completeVJ = merge(completeVJ, Jchain, by.x="Top.J.Gene", by.y="v.name", all.x=TRUE)
501
502 fltr = is.nan(completeVJ$relLength)
503 if(any(fltr, na.rm=T)){
504 completeVJ[fltr,"relLength"] = 1
505 }
506
496 VJList = split(completeVJ, f=completeVJ[,"Sample"]) 507 VJList = split(completeVJ, f=completeVJ[,"Sample"])
497 lapply(VJList, FUN=plotVJ) 508 lapply(VJList, FUN=plotVJ)
498 509
499 510
500 511
529 cartegianProductDJ = expand.grid(Top.D.Gene = Dchain$v.name, Top.J.Gene = Jchain$v.name, Sample = unique(inputdata$Sample)) 540 cartegianProductDJ = expand.grid(Top.D.Gene = Dchain$v.name, Top.J.Gene = Jchain$v.name, Sample = unique(inputdata$Sample))
530 541
531 completeDJ = merge(DandJCount, cartegianProductDJ, all.y=TRUE) 542 completeDJ = merge(DandJCount, cartegianProductDJ, all.y=TRUE)
532 completeDJ = merge(completeDJ, revDchain, by.x="Top.D.Gene", by.y="v.name", all.x=TRUE) 543 completeDJ = merge(completeDJ, revDchain, by.x="Top.D.Gene", by.y="v.name", all.x=TRUE)
533 completeDJ = merge(completeDJ, Jchain, by.x="Top.J.Gene", by.y="v.name", all.x=TRUE) 544 completeDJ = merge(completeDJ, Jchain, by.x="Top.J.Gene", by.y="v.name", all.x=TRUE)
545
546 fltr = is.nan(completeDJ$relLength)
547 if(any(fltr, na.rm=T)){
548 completeDJ[fltr,"relLength"] = 1
549 }
550
534 DJList = split(completeDJ, f=completeDJ[,"Sample"]) 551 DJList = split(completeDJ, f=completeDJ[,"Sample"])
535 lapply(DJList, FUN=plotDJ) 552 lapply(DJList, FUN=plotDJ)
536 } 553 }
537 554
538 555