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 <538...@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 > <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. ______________________________________________ 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.
