Mercurial > repos > davidvanzessen > argalaxy_tools

comparison report_clonality/RScript.r @ 14:15961ca8d9ce draft

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author davidvanzessen
date Tue, 20 Dec 2016 06:26:44 -0500
parents d3ebaa2d2fe0
children 02efa5764a0a
comparison
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13:d3ebaa2d2fe0 14:15961ca8d9ce
405 theme(axis.text.x = element_text(angle = 90, hjust = 1)) + 405 theme(axis.text.x = element_text(angle = 90, hjust = 1)) +
406 scale_fill_gradient(low="gold", high="blue", na.value="white") + 406 scale_fill_gradient(low="gold", high="blue", na.value="white") +
407 ggtitle(paste(unique(dat$Sample), " (N=" , sum(dat$Length, na.rm=T) ,")", sep="")) + 407 ggtitle(paste(unique(dat$Sample), " (N=" , sum(dat$Length, na.rm=T) ,")", sep="")) +
408 xlab("D genes") + 408 xlab("D genes") +
409 ylab("V Genes") + 409 ylab("V Genes") +
410 theme(panel.background = element_rect(fill = "white", colour="black"),text = element_text(size=15, colour="black"), axis.text.x = element_text(angle = 45, hjust = 1), panel.grid.major = element_line(colour = "gainsboro")) 410 theme(panel.background = element_rect(fill = "white", colour="black"),text = element_text(size=15, colour="black"), panel.grid.major = element_line(colour = "gainsboro"))
411 411
412 png(paste("HeatmapVD_", unique(dat[3])[1,1] , ".png", sep=""), width=150+(15*length(Dchain$v.name)), height=100+(15*length(Vchain$v.name))) 412 png(paste("HeatmapVD_", unique(dat[3])[1,1] , ".png", sep=""), width=150+(15*length(Dchain$v.name)), height=100+(15*length(Vchain$v.name)))
413 print(img) 413 print(img)
414 dev.off() 414 dev.off()
415 write.table(x=acast(dat, Top.V.Gene~Top.D.Gene, value.var="Length"), file=paste("HeatmapVD_", unique(dat[3])[1,1], ".csv", sep=""), sep=",",quote=F,row.names=T,col.names=NA) 415 write.table(x=acast(dat, Top.V.Gene~Top.D.Gene, value.var="Length"), file=paste("HeatmapVD_", unique(dat[3])[1,1], ".csv", sep=""), sep=",",quote=F,row.names=T,col.names=NA)
455 theme(axis.text.x = element_text(angle = 90, hjust = 1)) + 455 theme(axis.text.x = element_text(angle = 90, hjust = 1)) +
456 scale_fill_gradient(low="gold", high="blue", na.value="white") + 456 scale_fill_gradient(low="gold", high="blue", na.value="white") +
457 ggtitle(paste(unique(dat$Sample), " (N=" , sum(dat$Length, na.rm=T) ,")", sep="")) + 457 ggtitle(paste(unique(dat$Sample), " (N=" , sum(dat$Length, na.rm=T) ,")", sep="")) +
458 xlab("J genes") + 458 xlab("J genes") +
459 ylab("V Genes") + 459 ylab("V Genes") +
460 theme(panel.background = element_rect(fill = "white", colour="black"),text = element_text(size=15, colour="black"), axis.text.x = element_text(angle = 45, hjust = 1), panel.grid.major = element_line(colour = "gainsboro")) 460 theme(panel.background = element_rect(fill = "white", colour="black"),text = element_text(size=15, colour="black"), panel.grid.major = element_line(colour = "gainsboro"))
461 461
462 png(paste("HeatmapVJ_", unique(dat[3])[1,1] , ".png", sep=""), width=150+(15*length(Jchain$v.name)), height=100+(15*length(Vchain$v.name))) 462 png(paste("HeatmapVJ_", unique(dat[3])[1,1] , ".png", sep=""), width=150+(15*length(Jchain$v.name)), height=100+(15*length(Vchain$v.name)))
463 print(img) 463 print(img)
464 dev.off() 464 dev.off()
465 write.table(x=acast(dat, Top.V.Gene~Top.J.Gene, value.var="Length"), file=paste("HeatmapVJ_", unique(dat[3])[1,1], ".csv", sep=""), sep=",",quote=F,row.names=T,col.names=NA) 465 write.table(x=acast(dat, Top.V.Gene~Top.J.Gene, value.var="Length"), file=paste("HeatmapVJ_", unique(dat[3])[1,1], ".csv", sep=""), sep=",",quote=F,row.names=T,col.names=NA)
504 theme(axis.text.x = element_text(angle = 90, hjust = 1)) + 504 theme(axis.text.x = element_text(angle = 90, hjust = 1)) +
505 scale_fill_gradient(low="gold", high="blue", na.value="white") + 505 scale_fill_gradient(low="gold", high="blue", na.value="white") +
506 ggtitle(paste(unique(dat$Sample), " (N=" , sum(dat$Length, na.rm=T) ,")", sep="")) + 506 ggtitle(paste(unique(dat$Sample), " (N=" , sum(dat$Length, na.rm=T) ,")", sep="")) +
507 xlab("J genes") + 507 xlab("J genes") +
508 ylab("D Genes") + 508 ylab("D Genes") +
509 theme(panel.background = element_rect(fill = "white", colour="black"),text = element_text(size=15, colour="black"), axis.text.x = element_text(angle = 45, hjust = 1), panel.grid.major = element_line(colour = "gainsboro")) 509 theme(panel.background = element_rect(fill = "white", colour="black"),text = element_text(size=15, colour="black"), panel.grid.major = element_line(colour = "gainsboro"))
510 510
511 png(paste("HeatmapDJ_", unique(dat[3])[1,1] , ".png", sep=""), width=150+(15*length(Jchain$v.name)), height=100+(15*length(Dchain$v.name))) 511 png(paste("HeatmapDJ_", unique(dat[3])[1,1] , ".png", sep=""), width=150+(15*length(Jchain$v.name)), height=100+(15*length(Dchain$v.name)))
512 print(img) 512 print(img)
513 dev.off() 513 dev.off()
514 write.table(x=acast(dat, Top.D.Gene~Top.J.Gene, value.var="Length"), file=paste("HeatmapDJ_", unique(dat[3])[1,1], ".csv", sep=""), sep=",",quote=F,row.names=T,col.names=NA) 514 write.table(x=acast(dat, Top.D.Gene~Top.J.Gene, value.var="Length"), file=paste("HeatmapDJ_", unique(dat[3])[1,1], ".csv", sep=""), sep=",",quote=F,row.names=T,col.names=NA)