1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
|
`plot.isomap` <-
function (x, net = TRUE, n.col = "gray", type = "points", ...)
{
type <- match.arg(type, c("points", "text", "none"))
if (!net) {
pl <- ordiplot(x, display="sites", type = type, ...)
} else {
pl <- ordiplot(x, display = "sites", type = "none", ...)
z <- scores(pl, "sites")
k <- x$net
## recycle colour for points
n.col <- rep(n.col, length = nrow(z))
n.col <- col2rgb(n.col)/255
## get average of colours of connected points
n.col <- (n.col[,k[,1]] + n.col[,k[,2]])/2
n.col <- rgb(t(n.col))
segments(z[k[,1],1], z[k[,1],2], z[k[,2],1], z[k[,2],2], col=n.col)
if (type == "points")
points(pl, "sites", ...)
else if (type == "text")
ordilabel(pl, ...)
}
invisible(pl)
}
|
