Mercurial > repos > davidvanzessen > argalaxy_tools

comparison aa_histogram.r @ 57:16c7fc1c4bf8 draft

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author davidvanzessen
date Fri, 18 Mar 2016 07:50:34 -0400
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56:2eb94c08e550 57:16c7fc1c4bf8
1 library(ggplot2)
2
3 args <- commandArgs(trailingOnly = TRUE)
4
5 input = args[1]
6 outfile = args[2]
7
8 print("---------------- read input ----------------")
9
10 dat = read.table(input, sep="\t", fill=T, header=T, quote="")
11
12 print("---------------- as numeric ----------------")
13
14 mutations.at.position = as.numeric(dat[1,])
15 aa.at.position = as.numeric(dat[2,])
16
17 print("---------------- freq data.frame ----------------")
18
19 dat_freq = mutations.at.position / aa.at.position
20 dat_dt = data.frame(i=1:length(dat_freq), freq=dat_freq)
21
22 print("---------------- weird stuff ----------------")
23
24 options(width=220)
25
26 print(dat[,20:40])
27
28 print(dat_dt) #need this or it will fail????
29
30 print("---------------- plot ----------------")
31
32 m = ggplot(dat_dt, aes(x=i, y=freq)) + theme(axis.text.x = element_text(angle = 90, hjust = 1))
33 m = m + geom_histogram(stat="identity", colour = "black", fill = "darkgrey", alpha=0.8) + scale_x_continuous(breaks=1:length(dat_freq), labels=1:length(dat_freq))
34 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")
35 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")
36 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")
37 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")
38 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")
39 m = m + expand_limits(y=c(-0.1,1)) + xlab("AA position") + ylab("Frequency") + ggtitle("AA mutation frequency")
40
41 print("---------------- write/print ----------------")
42
43 write.table(dat_dt, paste(dirname(outfile), "/aa_histogram.txt", sep=""), sep="\t",quote=F,row.names=F,col.names=T)
44
45 png(filename=outfile, width=1280, height=720)
46 print(m)
47 dev.off()