##  Specify the colors for the different nucleotides (ACGTN)
colors <- c("blue", "red", "green", "yellow", "pink")

##  Define a custom function to tally base calls by position
nucDistrFromFastx <- function(df){

  ##  Define the range of values for the plot window
  xlim <- c(0, nrow(df)+1)
  ylim <- c(0, max(df$count))

  ##  Plot the nucleotide distributions counts
  par(mar=c(5,4,2,2)+0.1, xaxs="i", yaxs="i")
  plot(xlim, ylim, type="n", xlab="Read position", ylab="Number of nucleotides")
  for (i in 1:nrow(df)){
    ys <- c(0,
            df$A_Count[i],
            df$A_Count[i]+df$C_Count[i],
            df$A_Count[i]+df$C_Count[i]+df$G_Count[i],
            df$A_Count[i]+df$C_Count[i]+df$G_Count[i]+df$T_Count[i],
            df$A_Count[i]+df$C_Count[i]+df$G_Count[i]+df$T_Count[i]+df$N_Count[i]
            )

    ##  Apply colors
    for (j in 1:5){
      plot_rect(i, ys[j], ys[j+1], colors[j])
    }

    ##  Generate legend
    legend("topright", legend=c("A", "C", "G", "T", "N"), fill=colors)
  }
}

plot_rect <- function(x, y1, y2, col){
  polygon(x=c(x-0.4, x-0.4, x+0.4, x+0.4, x-0.4),
        y=c(y1, y2, y2, y1, y1),
        col=col)
}

##  Capture command line arguments
args <- (commandArgs(TRUE))

##  Read in tab-delimited file as a table
##  Use the first line as column headers
data <- read.table(args[1], head=TRUE, as.is=TRUE)

##  Apply user-defined output filename, if it was specified
if (length(args) > 1){
  outfile <- args[2]
} else {
  outfile <- paste(args[1], ".png", sep="")
}

##  Initialize PNG output file and specify dimensions
png(file=outfile, w=1000, h=500)

##  Call custom function to generate plot
nucDistrFromFastx(data)

##  Close output file
dev.off()