[R] plot hclust object

[Martin Maechler]

>>>>> Greg Snow <538280 at gmail.com>
>>>>>     on Mon, 27 Oct 2014 12:33:18 -0600 writes:

    > I don't know of any tools that automate this process.  For small
    > sample sizes it may be easiest to just do this by hand, for large
    > sample sizes that plot will probably be to complicated to make sense
    > of.  There may be a range of moderate sample sizes for which
    > automation (or partial automation) would be helpful.  The hclust
    > object has a component of "height" which is an indicator of the
    > distance between 2 components being combined into a cluster, you could
    > convert this into a distance matrix 

it has been known for many years how to do this; still, I have
only learned about it from Robert Gentleman (yes, one of the two
fathers of R), when we added the function 

	cophenetic() 
to R
which does exactly do this: 
Provide the distance matrix which is implicitly defined by a
hierarchical clustering.

Martin Maechler, ETH Zurich

    > (or extract the distance matrix used to do the clustering
    > if it is available) and then use multidimensional scaling
    > (cmdscale function is one option) to produce a 2
    > dimensional set of points.  Drawing the
    > circles/ellipses/ovals will be more difficult, possibly
    > generate a cloud of normal points, or a small circle,
    > around each point with the variability/radius low enough
    > that the clouds are unlikely to overlap, then find the
    > convex hull (chull function) for the points within a
    > cluster and draw that (it will be a polygon rather than a
    > smooth curve).  The gBuffer command in the rgeos package
    > may be another way to create polygons around the points in
    > a group.

    > On Mon, Oct 27, 2014 at 5:42 AM, David Feitosa <davidfeitosa at gmail.com> wrote:
    >> Hello!
    >> 
    >> I have a code that creates an hclust object.
    >> After the object creation I plot the object as a dendrogram,
    >> similar to the left image of this link:
    >> 
    >> http://www.cs.jhu.edu/~razvanm/fs-expedition/hclust-example.png
    >> 
    >> I would like to create another image, but similar to the right,
    >> as a set of nested  dots and elipses/circles.
    >> 
    >> Anybody knows how to do this?
    >> 
    >> Thanks in advance.
    >> 
    >> David Feitosa
    >> 
    >> (\_(\
    >> (=°;°)
    >> (("")("")
    >> 
    >> [[alternative HTML version deleted]]
    >> 
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    > -- 
    > Gregory (Greg) L. Snow Ph.D.
    > 538280 at gmail.com

    > ______________________________________________
    > R-help at r-project.org mailing list
    > https://stat.ethz.ch/mailman/listinfo/r-help
    > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
    > and provide commented, minimal, self-contained, reproducible code.