Mercurial > repos > davidvanzessen > mutation_analysis

comparison aa_histogram.r @ 109:0096cd454380 draft

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author davidvanzessen
date Thu, 14 Jul 2016 07:29:56 -0400
parents 6add3e66f4fa
children ade5cf6fd2dc
comparison
equal deleted inserted replaced
108:6add3e66f4fa 109:0096cd454380
46 m = m + annotate("segment", x = 65.5, y = -0.05, xend=104.5, yend=-0.05, colour="darkgreen", size=1) + annotate("text", x = 85, y = -0.1, label="FR3") 46 m = m + annotate("segment", x = 65.5, y = -0.05, xend=104.5, yend=-0.05, colour="darkgreen", size=1) + annotate("text", x = 85, y = -0.1, label="FR3")
47 m = m + expand_limits(y=c(-0.1,1)) + xlab("AA position") + ylab("Frequency") + ggtitle(paste(gene, "AA mutation frequency")) 47 m = m + expand_limits(y=c(-0.1,1)) + xlab("AA position") + ylab("Frequency") + ggtitle(paste(gene, "AA mutation frequency"))
48 48
49 print("---------------- write/print ----------------") 49 print("---------------- write/print ----------------")
50 50
51 png(filename=paste(outdir, "/aa_histogram_", gene, ".png", sep=""), width=1280, height=720)
52 print(m)
53 dev.off()
54
51 dat.sums = data.frame(index=1:length(mutations.at.position), mutations.at.position=mutations.at.position, aa.at.position=aa.at.position) 55 dat.sums = data.frame(index=1:length(mutations.at.position), mutations.at.position=mutations.at.position, aa.at.position=aa.at.position)
52 56
53 write.table(dat.sums, paste(outdir, "/aa_histogram_sum_", gene, ".txt", sep=""), sep="\t",quote=F,row.names=F,col.names=T) 57 write.table(dat.sums, paste(outdir, "/aa_histogram_sum_", gene, ".txt", sep=""), sep="\t",quote=F,row.names=F,col.names=T)
54 write.table(mutations.by.id.gene, paste(outdir, "/aa_histogram_count_", gene, ".txt", sep=""), sep="\t",quote=F,row.names=F,col.names=T) 58 write.table(mutations.by.id.gene, paste(outdir, "/aa_histogram_count_", gene, ".txt", sep=""), sep="\t",quote=F,row.names=F,col.names=T)
55 write.table(absent.aa.by.id.gene, paste(outdir, "/aa_histogram_absent_", gene, ".txt", sep=""), sep="\t",quote=F,row.names=F,col.names=T) 59 write.table(absent.aa.by.id.gene, paste(outdir, "/aa_histogram_absent_", gene, ".txt", sep=""), sep="\t",quote=F,row.names=F,col.names=T)
56 write.table(dat_dt, paste(outdir, "/aa_histogram_", gene, ".txt", sep=""), sep="\t",quote=F,row.names=F,col.names=T) 60 write.table(dat_dt, paste(outdir, "/aa_histogram_", gene, ".txt", sep=""), sep="\t",quote=F,row.names=F,col.names=T)
57 png(filename=paste(outdir, "/aa_histogram_", gene, ".png", sep=""), width=1280, height=720)
58 print(m)
59 dev.off()
60 } 61 }