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`plot.spantree` <-
function (x, ord, cex = 0.7, type = "p", labels, dlim, FUN = sammon,
...)
{
FUNname <- deparse(substitute(FUN))
FUN <- match.fun(FUN)
n <- x$n
if (missing(ord)) {
d <- cophenetic(x)
if (any(d<=0))
d[d<=0] <- min(d>0)/10
if (!missing(dlim))
d[d > dlim ] <- dlim
if (n > 2) {
## sammon needs extra care, for other cases we just try FUN(d)
if (FUNname == "sammon") {
y <- cmdscale(d)
dup <- duplicated(y)
if (any(dup))
y[dup, ] <- y[dup,] + runif(2*sum(dup), -0.01, 0.01)
ord <- FUN(d, y = y)
} else
ord <- FUN(d)
} else
ord <- cbind(seq_len(n), rep(0,n))
}
ord <- scores(ord, display = "sites", ...)
ordiArgAbsorber(ord, asp = 1, type = "n", FUN = "plot", ...)
lines(x, ord, ...)
if (type == "p" || type == "b")
ordiArgAbsorber(ord, cex = cex, FUN = "points", ...)
else if (type == "t") {
if (missing(labels))
labels <- x$labels
x <- scores(ord, display = "sites", ...)
ordiArgAbsorber(x, labels = labels, cex = cex, FUN = "ordilabel", ...)
}
ord <- list(sites = ord)
class(ord) <- "ordiplot"
invisible(ord)
}
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