Mercurial > repos > davidvanzessen > argalaxy_tools

comparison report_clonality/RScript.r @ 53:379856bef228 draft

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author davidvanzessen
date Fri, 29 Jan 2016 05:39:58 -0500
parents 371c568408e9
children 5ba0377b7737
comparison
equal deleted inserted replaced
52:371c568408e9 53:379856bef228
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)
459 459
460 if(any(fltr, na.rm=T)){ 460 fltr = is.nan(completeVD$relLength)
461 completeVD[fltr,"relLength"] = 1 461 if(any(fltr)){
462 } 462 completeVD[fltr,"relLength"] = 1
463 }
463 464
464 VDList = split(completeVD, f=completeVD[,"Sample"]) 465 VDList = split(completeVD, f=completeVD[,"Sample"])
465 lapply(VDList, FUN=plotVD) 466 lapply(VDList, FUN=plotVD)
466 } 467 }
467 468
498 completeVJ = merge(VandJCount, cartegianProductVJ, all.y=TRUE) 499 completeVJ = merge(VandJCount, cartegianProductVJ, all.y=TRUE)
499 completeVJ = merge(completeVJ, revVchain, by.x="Top.V.Gene", by.y="v.name", all.x=TRUE) 500 completeVJ = merge(completeVJ, revVchain, by.x="Top.V.Gene", by.y="v.name", all.x=TRUE)
500 completeVJ = merge(completeVJ, Jchain, by.x="Top.J.Gene", by.y="v.name", all.x=TRUE) 501 completeVJ = merge(completeVJ, Jchain, by.x="Top.J.Gene", by.y="v.name", all.x=TRUE)
501 502
502 fltr = is.nan(completeVJ$relLength) 503 fltr = is.nan(completeVJ$relLength)
503 if(any(fltr, na.rm=T)){ 504 if(any(fltr)){
504 completeVJ[fltr,"relLength"] = 1 505 completeVJ[fltr,"relLength"] = 1
505 } 506 }
506 507
507 VJList = split(completeVJ, f=completeVJ[,"Sample"]) 508 VJList = split(completeVJ, f=completeVJ[,"Sample"])
508 lapply(VJList, FUN=plotVJ) 509 lapply(VJList, FUN=plotVJ)
509 510
542 completeDJ = merge(DandJCount, cartegianProductDJ, all.y=TRUE) 543 completeDJ = merge(DandJCount, cartegianProductDJ, all.y=TRUE)
543 completeDJ = merge(completeDJ, revDchain, by.x="Top.D.Gene", by.y="v.name", all.x=TRUE) 544 completeDJ = merge(completeDJ, revDchain, by.x="Top.D.Gene", by.y="v.name", all.x=TRUE)
544 completeDJ = merge(completeDJ, Jchain, by.x="Top.J.Gene", by.y="v.name", all.x=TRUE) 545 completeDJ = merge(completeDJ, Jchain, by.x="Top.J.Gene", by.y="v.name", all.x=TRUE)
545 546
546 fltr = is.nan(completeDJ$relLength) 547 fltr = is.nan(completeDJ$relLength)
547 if(any(fltr, na.rm=T)){ 548 if(any(fltr)){
548 completeDJ[fltr,"relLength"] = 1 549 completeDJ[fltr, "relLength"] = 1
549 } 550 }
550 551
551 DJList = split(completeDJ, f=completeDJ[,"Sample"]) 552 DJList = split(completeDJ, f=completeDJ[,"Sample"])
552 lapply(DJList, FUN=plotDJ) 553 lapply(DJList, FUN=plotDJ)
553 } 554 }