[R] plot hclust object
Bert Gunter
gunter.berton at gene.com
Tue Oct 28 21:41:35 CET 2014
Copacetic cophenetics are a way
To better see much genetics.
;-)
-- Bert
Bert Gunter
Genentech Nonclinical Biostatistics
(650) 467-7374
"Data is not information. Information is not knowledge. And knowledge
is certainly not wisdom."
Clifford Stoll
On Tue, Oct 28, 2014 at 1:28 PM, Greg Snow <538280 at gmail.com> wrote:
> I would suggest links to cophenetic on the help pages for dendrogram
> and possibly plot.hclust and related functions.
>
> I was not complaining. I always enjoy learning new things, it is a
> testament to the breadth and depth of R that even after more than 25
> years using S and R, that I can still be pleasantly surprised with
> functions that I did not know about.
>
> The word cophenetic just has a nice ring to it, has a similar rhythm
> and rhymes with copacetic (I think I will challenge my writer
> co-worker to come up with a poem including both words). I can see
> some of the origin of the word in genetics, but dropped in casual
> conversation it could be interpreted to mean any number of things. I
> may ask my wife when I get home if she is feeling cophenetic and want
> to cluster after the kids are in bed (though I should be careful not
> to agnes, daisy, pam, etc. or she may choose snuggling with the cats
> instead of me as her clustering).
>
> On Tue, Oct 28, 2014 at 12:26 PM, Martin Maechler
> <maechler at stat.math.ethz.ch> wrote:
>>>>>>> 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
>
>
>
> --
> 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.
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