Mercurial > repos > davidvanzessen > mutation_analysis

comparison aa_histogram.r @ 105:e4957ad476a2 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author davidvanzessen
date Thu, 23 Jun 2016 03:58:03 -0400
parents 603a10976e9c
children 01c9993865af
comparison
equal deleted inserted replaced
104:603a10976e9c 105:e4957ad476a2
18 print("---------------- freq data.frame ----------------") 18 print("---------------- freq data.frame ----------------")
19 19
20 dat_freq = mutations.at.position / aa.at.position 20 dat_freq = mutations.at.position / aa.at.position
21 dat_dt = data.frame(i=1:length(dat_freq), freq=dat_freq) 21 dat_dt = data.frame(i=1:length(dat_freq), freq=dat_freq)
22 22
23 print("---------------- weird stuff ----------------")
24
25 options(width=220)
26
27 print(dat[,20:40])
28
29 print(dat_dt) #need this or it will fail????
30
31 print("---------------- plot ----------------") 23 print("---------------- plot ----------------")
32
33 #also need these two, I don't even know...
34 print(paste("dat_freq", length(dat_freq)))
35 print(paste("dat_dt", nrow(dat_dt)))
36 24
37 m = ggplot(dat_dt, aes(x=i, y=freq)) + theme(axis.text.x = element_text(angle = 90, hjust = 1)) 25 m = ggplot(dat_dt, aes(x=i, y=freq)) + theme(axis.text.x = element_text(angle = 90, hjust = 1))
38 m = m + geom_bar(stat="identity", colour = "black", fill = "darkgrey", alpha=0.8) + scale_x_continuous(breaks=1:length(dat_freq), labels=1:length(dat_freq)) 26 m = m + geom_bar(stat="identity", colour = "black", fill = "darkgrey", alpha=0.8) + scale_x_continuous(breaks=1:length(dat_freq), labels=1:length(dat_freq))
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") 27 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")
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") 28 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")
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") 31 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")
44 m = m + expand_limits(y=c(-0.1,1)) + xlab("AA position") + ylab("Frequency") + ggtitle(paste(gene, "AA mutation frequency")) 32 m = m + expand_limits(y=c(-0.1,1)) + xlab("AA position") + ylab("Frequency") + ggtitle(paste(gene, "AA mutation frequency"))
45 33
46 print("---------------- write/print ----------------") 34 print("---------------- write/print ----------------")
47 35
48 print("writing dat_dt") #need this
49 write.table(dat_dt, paste(dirname(outfile), "/aa_histogram_", gene, ".txt", sep=""), sep="\t",quote=F,row.names=F,col.names=T) 36 write.table(dat_dt, paste(dirname(outfile), "/aa_histogram_", gene, ".txt", sep=""), sep="\t",quote=F,row.names=F,col.names=T)
50 print("writing png") #also need this, file is haunted
51 png(filename=outfile, width=1280, height=720) 37 png(filename=outfile, width=1280, height=720)
52 print(m) 38 print(m)
53 dev.off() 39 dev.off()