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dotPlot <- function(seq1, seq2, wsize = 1, wstep = 1, nmatch = 1, col = c("white", "black"),
xlab = deparse(substitute(seq1)), ylab = deparse(substitute(seq2)), ...){
#
# Check arguments:
#
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")
#
# sliding window on sequences:
#
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 ){
# perfect match case
xy <- outer(wseq1, wseq2, "==")
} else {
# partial match case
"%==%" <- function(x, y) colSums(sapply(x, s2c) == sapply(y, s2c)) >= nmatch
xy <- outer(wseq1, wseq2, "%==%")
}
image(x = seq(from = 1, to = length(seq1), length = length(wseq1)),
y = seq(from = 1, to = length(seq2), length = length(wseq2)),
z = xy, col = col, xlab = xlab, ylab = ylab, ...)
box()
}
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