R/cpgDensityPlot.R

In markrobinsonuzh/Repitools: Epigenomic tools

setGeneric("cpgDensityPlot", function(x, ...){standardGeneric("cpgDensityPlot")})

setMethod("cpgDensityPlot", "GRangesList",
    function(x, cols = rainbow(length(x)), xlim = c(0, 20), lty = 1, lwd = 1,
             main = "CpG Density Plot", verbose = TRUE, ...)
{
    if (length(cols) != length(x)) stop("x and cols must have the same number of elements.")
    if (verbose) message("Calculating CpG density")
    x.cpg <- cpgDensityCalc(x, verbose = verbose, ...)
    x.den <- lapply(x.cpg, density)
    ymax <- max(sapply(x.den, function(u) max(u$y)))
    plot(x = x.den[[1]]$x, y = x.den[[1]]$y, type = 'l', col = cols[1], xlim=xlim,
         ylim = c(0, ymax), main = main, ylab = "Frequency", xlab = "CpG Density of reads",
         lty = lty, lwd = lwd)
    if (length(x) > 1)
    {
        for (i in 2:length(x)) {
            lines(x = x.den[[i]]$x, y = x.den[[i]]$y, col = cols[i], lty = lty, lwd = lwd)
        }
    }
    legend("topright", col = cols, legend = names(x), lty = lty, lwd = lwd)
    invisible(x.cpg)
})