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81
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1 library(ggplot2)
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2
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3 args <- commandArgs(trailingOnly = TRUE)
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4
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5 mutations.by.id.file = args[1]
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6 absent.aa.by.id.file = args[2]
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7 genes = strsplit(args[3], ",")[[1]]
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8 genes = c(genes, "")
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9 outdir = args[4]
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10
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11
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12 print("---------------- read input ----------------")
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13
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14 mutations.by.id = read.table(mutations.by.id.file, sep="\t", fill=T, header=T, quote="")
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15 absent.aa.by.id = read.table(absent.aa.by.id.file, sep="\t", fill=T, header=T, quote="")
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16
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17 for(gene in genes){
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18 graph.title = paste(gene, "AA mutation frequency")
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19 if(gene == ""){
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20 mutations.by.id.gene = mutations.by.id[!grepl("unmatched", mutations.by.id$best_match),]
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21 absent.aa.by.id.gene = absent.aa.by.id[!grepl("unmatched", absent.aa.by.id$best_match),]
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22
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23 graph.title = "AA mutation frequency all"
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24 } else {
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25 mutations.by.id.gene = mutations.by.id[grepl(paste("^", gene, sep=""), mutations.by.id$best_match),]
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26 absent.aa.by.id.gene = absent.aa.by.id[grepl(paste("^", gene, sep=""), absent.aa.by.id$best_match),]
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27 }
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28 print(paste("nrow", gene, nrow(absent.aa.by.id.gene)))
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29 if(nrow(mutations.by.id.gene) == 0){
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30 next
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31 }
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32
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33 mutations.at.position = colSums(mutations.by.id.gene[,-c(1,2)])
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34 aa.at.position = colSums(absent.aa.by.id.gene[,-c(1,2,3,4)])
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35
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36 dat_freq = mutations.at.position / aa.at.position
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37 dat_freq[is.na(dat_freq)] = 0
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38 dat_dt = data.frame(i=1:length(dat_freq), freq=dat_freq)
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39
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40
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41 print("---------------- plot ----------------")
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42
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43 m = ggplot(dat_dt, aes(x=i, y=freq)) + theme(axis.text.x = element_text(angle = 90, hjust = 1), text = element_text(size=13, colour="black"))
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44 m = m + geom_bar(stat="identity", colour = "black", fill = "darkgrey", alpha=0.8) + scale_x_continuous(breaks=dat_dt$i, labels=dat_dt$i)
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45 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")
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46 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")
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47 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")
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48 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")
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49 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")
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50 m = m + expand_limits(y=c(-0.1,1)) + xlab("AA position") + ylab("Frequency") + ggtitle(graph.title)
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51 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())
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52 #m = m + scale_colour_manual(values=c("black"))
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53
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54 print("---------------- write/print ----------------")
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55
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56
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57 dat.sums = data.frame(index=1:length(mutations.at.position), mutations.at.position=mutations.at.position, aa.at.position=aa.at.position)
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58
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59 write.table(dat.sums, paste(outdir, "/aa_histogram_sum_", gene, ".txt", sep=""), sep="\t",quote=F,row.names=F,col.names=T)
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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)
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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)
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62 write.table(dat_dt, paste(outdir, "/aa_histogram_", gene, ".txt", sep=""), sep="\t",quote=F,row.names=F,col.names=T)
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63
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64 png(filename=paste(outdir, "/aa_histogram_", gene, ".png", sep=""), width=1280, height=720)
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65 print(m)
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66 dev.off()
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67
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68 ggsave(paste(outdir, "/aa_histogram_", gene, ".pdf", sep=""), m, width=14, height=7)
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69 }
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