[R] From Distance Matrix to 2D coordinates

Sarah Goslee sarah.goslee at gmail.com
Thu Dec 15 19:16:56 CET 2011

That's exactly what ordination is for (not clustering).

I'd try principal coordinates analysis, or non-metric multidimensional
scaling, depending on whether the dissimilarity you'v been given is
metric or nonmetric.

There are implementations of both in the ecodist package, and in
various other packages as well, so you have lots of choice.


On Thu, Dec 15, 2011 at 1:08 PM, Lorenzo Isella
<lorenzo.isella at gmail.com> wrote:
> Dear All,
> I am struggling with the following problem: I am given a NxN symmetric
> matrix P ( P[i,i]=0, i=1...N and P[i,j]>0 for i!=j) which stands for the
> relative distances of N points.
> I would like use it to get the coordinates of the N points in a 2D plane. Of
> course, the solution is not unique (given one solution, I can translate or
> rotate all the points by the same amount and generate another solution), but
> any correct solution will do for me.
> Any idea about how I can achieve that? Is there any clustering package that
> can help me?
> Many thanks.
> Lorenzo

Sarah Goslee

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