21 lines
776 B
R
Executable File
21 lines
776 B
R
Executable File
#!/broad/tools/apps/R-2.6.0/bin/Rscript
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args <- commandArgs(TRUE)
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verbose = TRUE
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input = args[1]
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#X11(width=7, height=14)
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#outfile = paste(input, ".qual_diff_v_cycle.png", sep="")
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#png(outfile, height=7, width=7, units="in", res=72) #height=1000, width=680)
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outfile = paste(input, ".qual_diff_v_cycle.pdf", sep="")
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pdf(outfile, height=7, width=7)
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par(cex=1.1)
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c <- read.table(input, header=T)
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d.good <- c[c$nMismatches >= 100,]
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d.100 <- c[c$nMismatches < 100,]
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plot(d.good$Cycle, d.good$Qempirical_Qreported, type="l", ylab="Empirical - Reported Quality", xlab="Cycle", col="blue", ylim=c(-10, 10))
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points(d.100$Cycle, d.100$Qempirical_Qreported, type="p", col="lightblue", pch=3)
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#points(d.1000$Cycle, d.1000$Qempirical_Qreported, type="p", col="cornflowerblue", pch=16)
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