[R] plot hclust object

[Martin Maechler]

>>>>> Greg Snow <538280 at gmail.com>
>>>>>     on Tue, 28 Oct 2014 10:31:27 -0600 writes:

    > Thanks Martin,  It is always great to learn that I don't need to
    > reinvent the wheel (especially when I learn that before reinventing).

    > Do you know if there are any help pages that point to cophenetic (see
    > also or other sections).  Maybe it is just the way that my brain is
    > wired (along with being a dabbler, but not expert at cluster
    > analysis), but for some reason the word cophenetic never occurred to
    > me as a search term while thinking about how to create the requested plot.

I understand.  Indeed, the world is never going to be perfect, nor is R.

Currently the only link to 'cophenetic' is in  ?reorder.dendrogram
and it's easy possible you'd neither have seen that page.

I strongly agree that more \link's would be useful in general
and in particular for cophenetic. I'm happy to take suggestions,
notably if they already use  Rd syntax ... ;-)

Martin

    > On Tue, Oct 28, 2014 at 9:31 AM, Martin Maechler
    > <maechler at stat.math.ethz.ch> wrote:
    >>>>>>> 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]]
    >> >>
    >> >> ______________________________________________
    >> >> 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.
    >> 
    >> 
    >> 
    >> > --
    >> > 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.



    > -- 
    > Gregory (Greg) L. Snow Ph.D.
    > 538280 at gmail.com