>>>>> Greg Snow <538...@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
> <maech...@stat.math.ethz.ch> wrote:
>>>>>>> Greg Snow <538...@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
<davidfeit...@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@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.
>> > 538...@gmail.com
>>
>> > ______________________________________________
>> > R-help@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.
> 538...@gmail.com
______________________________________________
R-help@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.
