dot_plot_data <- function (seq1, seq2, wsize = 1, wstep = 1, nmatch = 1,...) {
	
	cat("Modification of dotPlot function in package seqinr.\n")
	cat("The function returns a matrix for plotting.\n")
	cat("Row names contain Sequence1, Col names Sequence2.\n")
	cat("Use the reshape2 package to convert and plot with ggplot2 and geom_raster.\n")

	require(seqinr)
	
	if (nchar(seq1[1]) > 1) 
		stop("seq1 should be provided as a vector of single chars")
    if (nchar(seq2[1]) > 1) 
        stop("seq2 should be provided as a vector of single chars")
    if (wsize < 1) 
        stop("non allowed value for wsize")
    if (wstep < 1) 
        stop("non allowed value for wstep")
    if (nmatch < 1) 
        stop("non allowed value for nmatch")
    if (nmatch > wsize) 
        stop("nmatch > wsize is not allowed")
    
    mkwin <- function(seq, wsize, wstep) {
        sapply(seq(from = 1, to = length(seq) - wsize + 1, by = wstep), 
            function(i) c2s(seq[i:(i + wsize - 1)]))
    }
    
    wseq1 <- mkwin(seq1, wsize, wstep)
    wseq2 <- mkwin(seq2, wsize, wstep)
    
    if (nmatch == wsize) {
        xy <- outer(wseq1, wseq2, "==")
    }
    else {
        "%==%" <- function(x, y) colSums(sapply(x, s2c) == sapply(y, 
            s2c)) >= nmatch
        xy <- outer(wseq1, wseq2, "%==%")
    }

    # xy is a matrix, write row names and column names for reference
    colnames(xy) <- wseq2
    rownames(xy) <- wseq1
    return(xy)
}