Mercurial > repos > davidvanzessen > mutation_analysis

comparison aa_histogram.r @ 104:603a10976e9c draft

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Uploaded
author davidvanzessen
date Wed, 22 Jun 2016 10:07:28 -0400
parents e6bc976760d4
children e4957ad476a2
comparison
equal deleted inserted replaced
103:e21cbe15381f 104:603a10976e9c
2 2
3 args <- commandArgs(trailingOnly = TRUE) 3 args <- commandArgs(trailingOnly = TRUE)
4 4
5 input = args[1] 5 input = args[1]
6 outfile = args[2] 6 outfile = args[2]
7 gene = args[3]
7 8
8 print("---------------- read input ----------------") 9 print("---------------- read input ----------------")
9 10
10 dat = read.table(input, sep="\t", fill=T, header=T, quote="") 11 dat = read.table(input, sep="\t", fill=T, header=T, quote="")
11 12
38 m = m + annotate("segment", x = 0.5, y = -0.05, xend=26.5, yend=-0.05, colour="darkgreen", size=1) + annotate("text", x = 13, y = -0.1, label="FR1") 39 m = m + annotate("segment", x = 0.5, y = -0.05, xend=26.5, yend=-0.05, colour="darkgreen", size=1) + annotate("text", x = 13, y = -0.1, label="FR1")
39 m = m + annotate("segment", x = 26.5, y = -0.07, xend=38.5, yend=-0.07, colour="darkblue", size=1) + annotate("text", x = 32.5, y = -0.15, label="CDR1") 40 m = m + annotate("segment", x = 26.5, y = -0.07, xend=38.5, yend=-0.07, colour="darkblue", size=1) + annotate("text", x = 32.5, y = -0.15, label="CDR1")
40 m = m + annotate("segment", x = 38.5, y = -0.05, xend=55.5, yend=-0.05, colour="darkgreen", size=1) + annotate("text", x = 47, y = -0.1, label="FR2") 41 m = m + annotate("segment", x = 38.5, y = -0.05, xend=55.5, yend=-0.05, colour="darkgreen", size=1) + annotate("text", x = 47, y = -0.1, label="FR2")
41 m = m + annotate("segment", x = 55.5, y = -0.07, xend=65.5, yend=-0.07, colour="darkblue", size=1) + annotate("text", x = 60.5, y = -0.15, label="CDR2") 42 m = m + annotate("segment", x = 55.5, y = -0.07, xend=65.5, yend=-0.07, colour="darkblue", size=1) + annotate("text", x = 60.5, y = -0.15, label="CDR2")
42 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") 43 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")
43 m = m + expand_limits(y=c(-0.1,1)) + xlab("AA position") + ylab("Frequency") + ggtitle("AA mutation frequency") 44 m = m + expand_limits(y=c(-0.1,1)) + xlab("AA position") + ylab("Frequency") + ggtitle(paste(gene, "AA mutation frequency"))
44 45
45 print("---------------- write/print ----------------") 46 print("---------------- write/print ----------------")
46 47
47 print("writing dat_dt") #need this 48 print("writing dat_dt") #need this
48 write.table(dat_dt, paste(dirname(outfile), "/aa_histogram.txt", sep=""), sep="\t",quote=F,row.names=F,col.names=T) 49 write.table(dat_dt, paste(dirname(outfile), "/aa_histogram_", gene, ".txt", sep=""), sep="\t",quote=F,row.names=F,col.names=T)
49 print("writing png") #also need this, file is haunted 50 print("writing png") #also need this, file is haunted
50 png(filename=outfile, width=1280, height=720) 51 png(filename=outfile, width=1280, height=720)
51 print(m) 52 print(m)
52 dev.off() 53 dev.off()