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 <maech...@stat.math.ethz.ch> wrote: >>>>>> 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 -- 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.
