# plot data being output from the quartet.pl Perl script

data <- read.table("quartet.out", sep = "\t", header = TRUE)

# number of lines
lines <- length(data$bin)

# find out about the maximum count for haplomaternal
ymax <- max(data$haplomaternal)

# define a vector of colours
colours <- c("red", "yellow", "green", "blue")

# make an empty plot
plot(0, type = "n", xlim = c(0, lines), ylim = c(0, 
    ymax), ylab = "Counts", xlab = "Bin")

# plot the data
for (i in (1:lines)) {
    # identify the column with the maximum value using the
    # function which.max()
    xmax = which.max(c(data$identical[i], data$haplopaternal[i], 
        data$haplomaternal[i], data$nonidentical[i]))
    
    # plot the line
    lines(c(i, i), c(0, data[i, xmax + 1]), col = colours[xmax], 
        lw = 1)
}