annotate aa_histogram.r @ 0:c33d93683a09 draft

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1 library(ggplot2)
2 
3 args <- commandArgs(trailingOnly = TRUE)
4 
5 mutations.by.id.file = args[1]
6 absent.aa.by.id.file = args[2]
7 genes = strsplit(args[3], ",")[[1]]
8 genes = c(genes, "")
9 outdir = args[4]
10 
11 
12 print("---------------- read input ----------------")
13 
14 mutations.by.id = read.table(mutations.by.id.file, sep="\t", fill=T, header=T, quote="")
15 absent.aa.by.id = read.table(absent.aa.by.id.file, sep="\t", fill=T, header=T, quote="")
16 
17 for(gene in genes){
18 
19         if(gene == ""){
20                 mutations.by.id.gene = mutations.by.id[!grepl("unmatched", mutations.by.id$best_match),]
21                 absent.aa.by.id.gene = absent.aa.by.id[!grepl("unmatched", absent.aa.by.id$best_match),]
22         } else {
23                 mutations.by.id.gene = mutations.by.id[grepl(paste("^", gene, sep=""), mutations.by.id$best_match),]
24                 absent.aa.by.id.gene = absent.aa.by.id[grepl(paste("^", gene, sep=""), absent.aa.by.id$best_match),]
25         }
26         print(paste("nrow", gene, nrow(absent.aa.by.id.gene)))
27         if(nrow(mutations.by.id.gene) == 0){
28                 next
29         }
30 
31         mutations.at.position = colSums(mutations.by.id.gene[,-c(1,2)])
32         aa.at.position = colSums(absent.aa.by.id.gene[,-c(1,2,3,4)])
33 
34         dat_freq = mutations.at.position / aa.at.position
35         dat_freq[is.na(dat_freq)] = 0
36         dat_dt = data.frame(i=1:length(dat_freq), freq=dat_freq)
37 
38         print("---------------- plot ----------------")
39 
40         m = ggplot(dat_dt, aes(x=i, y=freq)) + theme(axis.text.x = element_text(angle = 90, hjust = 1))
41         m = m + geom_bar(stat="identity", colour = "black", fill = "darkgrey", alpha=0.8) + scale_x_continuous(breaks=dat_dt$i, labels=dat_dt$i)
42         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")
43         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")
44         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")
45         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")
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")) 
48         m = m + theme(panel.background = element_rect(fill = "white", colour="black"), panel.grid.major.y = element_line(colour = "black"), panel.grid.major.x = element_blank())
49         m = m + scale_colour_manual(values=c("black"))
50 
51         print("---------------- write/print ----------------")
52 
53         png(filename=paste(outdir, "/aa_histogram_", gene, ".png", sep=""), width=1280, height=720)
54         print(m)
55         dev.off()
56 
57         dat.sums = data.frame(index=1:length(mutations.at.position), mutations.at.position=mutations.at.position, aa.at.position=aa.at.position)
58 
59         write.table(dat.sums, paste(outdir, "/aa_histogram_sum_", gene, ".txt", sep=""), sep="\t",quote=F,row.names=F,col.names=T)
60         write.table(mutations.by.id.gene, paste(outdir, "/aa_histogram_count_", gene, ".txt", sep=""), sep="\t",quote=F,row.names=F,col.names=T)
61         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)
62         write.table(dat_dt, paste(outdir, "/aa_histogram_", gene, ".txt", sep=""), sep="\t",quote=F,row.names=F,col.names=T)
63 }