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  # The MIT License                                                               #
  # Copyright (c) 2018 Fulcrum Genomics LLC                                       #
  # Permission is hereby granted, free of charge, to any person obtaining a copy  #
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  # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,      #
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  # THE SOFTWARE.                                                                 #
  #################################################################################
  
  # R script to generate QC plots from the FindSwitchbackReads tool
  
  options(warn = -1) # Don't emit warnings, only errors
  library(ggplot2)
  
  args        = commandArgs(trailingOnly=T)
  name        = args[1]
  lengthsFile = args[2]
  offsetsFile = args[3]
  gapsFile    = args[4]
  outputFile  = args[5]
  
  pdf(outputFile, width=11, height=8.5)
  
  # Standard colors
  files  = c(lengthsFile, offsetsFile, gapsFile)
  labels = c("Length of Switchback", "Switchback Offset", "Tandem Switchback Gap")
  colors = c("#2E9DD7", "#155936", "firebrick3")
  
  for (i in c(1,2,3)) {
    file  = files[i]
    color = colors[i]
    xlab  = labels[i]
  
    data = read.table(file, sep="\t", header=T)
    names(data)[1] = "key"
    plot = ggplot(data) + aes(x=key, y=count) + 
      scale_y_continuous(limits=c(0, NA)) +
      geom_bar(stat="identity", color=color, fill=color) +
      labs(x=xlab, y="Number of Templates", title=paste("Distribution of", xlab, "in", name)) +
      theme(plot.title = element_text(hjust = 0.5))
    
    print(plot)
  }
  
  dev.off()
  