myplotCophylo2 <- function (x, y, assoc = assoc, use.edge.length = use.edge.length, 
    space = space, length.line = length.line, gap = gap, type = type, 
    return = return, col = col, lwd = lwd, lty = lty, show.atip.label = show.atip.label, show.btip.label = show.btip.label, font = font, col.atip.label = col.atip.label, col.btip.label = col.btip.label,...) 
{
    # gap : a value specifying the distance between the tips of the phylogeny and the lines.
    # space a positive value that specifies the distance between the two trees.
    # length.line: a positive value that specifies the length of the horizontal line associated to each taxa. Default is 1.
    
    res <- list()
    left <- max(nchar(x$tip.label, type = "width")) + length.line
    right <- max(nchar(y$tip.label, type = "width")) + length.line
    left <- length.line
    right <- length.line
	space.min <- left + right + gap * 2
    if ((space <= 0) || (space < space.min)) 
        space <- space.min
    N.tip.x <- Ntip(x)
    N.tip.y <- Ntip(y)
    res$N.tip.x <- N.tip.x
    res$N.tip.y <- N.tip.y
    
    a <- plotPhyloCoor(x, use.edge.length = use.edge.length, 
        type = type)
    res$a <- a
    b <- plotPhyloCoor(y, use.edge.length = use.edge.length, 
        direction = "leftwards", type = type)
        
    a[, 2] <- a[, 2] - min(a[, 2])
    b[, 2] <- b[, 2] - min(b[, 2])
    res$b <- b
    b2 <- b
    b2[, 1] <- b[1:nrow(b), 1] * (max(a[, 1])/max(b[, 1])) + 
        space + max(a[, 1])
    b2[, 2] <- b[1:nrow(b), 2] * (max(a[, 2])/max(b[, 2]))
    res$b2 <- b2
    c <- matrix(ncol = 2, nrow = nrow(a) + nrow(b))
    c[1:nrow(a), ] <- a[1:nrow(a), ]
    c[nrow(a) + 1:nrow(b), 1] <- b2[, 1]
    c[nrow(a) + 1:nrow(b), 2] <- b2[, 2]
    res$c <- c
    plot(c, type = "n", xlim = NULL, ylim = NULL, log = "", main = NULL, 
        sub = NULL, xlab = NULL, ylab = NULL, ann = FALSE, axes = FALSE, 
        frame.plot = FALSE)
    if (type == "cladogram") {
        for (i in 1:(nrow(a) - 1)) segments(a[x$edge[i, 1], 1], 
            a[x$edge[i, 1], 2], a[x$edge[i, 2], 1], a[x$edge[i, 
                2], 2], col = "red")
        for (i in 1:(nrow(b) - 1)) segments(b2[y$edge[i, 1], 
            1], b2[y$edge[i, 1], 2], b2[y$edge[i, 2], 1], b2[y$edge[i, 
            2], 2])
    }
    # tracer des arbres
    if (type == "phylogram") {
        for (i in (N.tip.x + 1):nrow(a)) {
            l <- length(x$edge[x$edge[, 1] == i, ][, 1])
            for (j in 1:l) {
                segments(a[x$edge[x$edge[, 1] == i, ][1, 1], 
                  1], a[x$edge[x$edge[, 1] == i, 2], 2][1], a[x$edge[x$edge[, 
                  1] == i, ][1, 1], 1], a[x$edge[x$edge[, 1] == 
                  i, 2], 2][j])
                segments(a[x$edge[x$edge[, 1] == i, ][1, 1], 
                  1], a[x$edge[x$edge[, 1] == i, 2], 2][j], a[x$edge[x$edge[, 
                  1] == i, 2], 1][j], a[x$edge[x$edge[, 1] == 
                  i, 2], 2][j])
            }
        }
        for (i in (N.tip.y + 1):nrow(b)) {
            l <- length(y$edge[y$edge[, 1] == i, ][, 1])
            for (j in 1:l) {
                segments(b2[y$edge[y$edge[, 1] == i, ][1, 1], 
                  1], b2[y$edge[y$edge[, 1] == i, 2], 2][1], 
                  b2[y$edge[y$edge[, 1] == i, ][1, 1], 1], b2[y$edge[y$edge[, 
                    1] == i, 2], 2][j])
                segments(b2[y$edge[y$edge[, 1] == i, ][1, 1], 
                  1], b2[y$edge[y$edge[, 1] == i, 2], 2][j], 
                  b2[y$edge[y$edge[, 1] == i, 2], 1][j], b2[y$edge[y$edge[, 
                    1] == i, 2], 2][j])
            }
        }
    }
    if (show.atip.label) {
        text(a[1:N.tip.x, ], cex = 0.5, font = font, pos = 4, labels = x$tip.label, col=col.atip.label)
	}
    if (show.btip.label) {
        text(b2[1:N.tip.y, ], cex = 0.5, font = font, pos = 2, labels = y$tip.label, col=col.btip.label)
    }
    lsa <- 1:N.tip.x
    lsb <- 1:N.tip.y
    decx <- array(nrow(assoc))
    decy <- array(nrow(assoc))
    if (length(col) == 1) 
        colors <- c(rep(col, nrow(assoc)))
    else if (length(col) >= nrow(assoc)) 
        colors <- col
    else colors <- c(rep(col, as.integer(nrow(assoc)/length(col)) + 
        1))
    if (length(lwd) == 1) 
        lwidths <- c(rep(lwd, nrow(assoc)))
    else if (length(lwd) >= nrow(assoc)) 
        lwidths <- lwd
    else lwidths <- c(rep(lwd, as.integer(nrow(assoc)/length(lwd)) + 
        1))
    if (length(lty) == 1) 
        ltype <- c(rep(lty, nrow(assoc)))
    else if (length(lty) >= nrow(assoc)) 
        ltype <- lty
    else ltype <- c(rep(lty, as.integer(nrow(assoc)/length(lty)) + 
        1))
    
    # plot linker between tips 
    ecartmax <-  0  
    for (i in 1:nrow(assoc)) {
		ecartmax <- max(abs(a[lsa[x$tip.label == assoc[i, 1]], 2] - b2[lsb[y$tip.label == assoc[i, 2]], 2]), ecartmax)
    }
	
	mycolor <- rev(heat.colors(ecartmax+1, alpha = 1))
	#mycolor <- rev(grey.colors(ecartmax+1, start = 0.5, end = 1, gamma = 2.2))
	
    for (i in 1:nrow(assoc)) {
#~         if (show.tip.label) {
#~             decx[i] <- strwidth(x$tip.label[lsa[x$tip.label == 
#~                 assoc[i, 1]]])
#~             decy[i] <- strwidth(y$tip.label[lsb[y$tip.label == 
#~                 assoc[i, 2]]])
#~         }
#~         else {
            decx[i] <- decy[i] <- 0
#~         }
		colors[i] = mycolor[abs(a[lsa[x$tip.label == assoc[i, 1]], 2] - b2[lsb[y$tip.label == assoc[i, 2]], 2])+1]
 		colors[i] = 'red'
        # left segment
       segments(a[lsa[x$tip.label == assoc[i, 1]], 1] + decx[i] + 
            gap, a[lsa[x$tip.label == assoc[i, 1]], 2], a[lsa[x$tip.label == 
            assoc[i, 1]], 1] + gap + left, a[lsa[x$tip.label == 
            assoc[i, 1]], 2], col = colors[i], lwd = lwidths[i], 
            lty = ltype[i])
        # right segment
        segments(b2[lsb[y$tip.label == assoc[i, 2]], 1] - (decy[i] + 
            gap), b2[lsb[y$tip.label == assoc[i, 2]], 2], b2[lsb[y$tip.label == 
            assoc[i, 2]], 1] - (gap + right), b2[lsb[y$tip.label == 
            assoc[i, 2]], 2], col = colors[i], lwd = lwidths[i], 
            lty = ltype[i])
        # center segment
        segments(a[lsa[x$tip.label == assoc[i, 1]], 1] + gap + 
            left, a[lsa[x$tip.label == assoc[i, 1]], 2], b2[lsb[y$tip.label == 
            assoc[i, 2]], 1] - (gap + right), b2[lsb[y$tip.label == 
            assoc[i, 2]], 2], col = colors[i], lwd = lwidths[i], 
            lty = ltype[i])
    }
    if (return == TRUE) 
        return(res)
}