The blog Getting Genetics Done features tips for analyzing genomic data, such as this recent post on hierarchical clustering with R using the hclust function. One of the interesting wrinkles with genomic data is that there will generally be many clusters, in which case the traditional tree representation is likely to be an unreadable "fuzzball":
The post gives some useful tips on how to export the tree data from R and use specialized software to create alternate visualizations, like this circular cladogram:
Getting Genetics Done: Hierarchical Clustering in R
In the first image I can see the clusters, but not the labels.
In the circular image I can see the labels, but not the clusters (very easily).
Where's the "linked brushing" version of the two graphs...?
Posted by: Kevin Wright | September 14, 2009 at 12:47
I just thought I should mention that this is my favourite blog. I know, hyperbole, you think. But no: I learn more from this blog about R than from the now weighty shelves of R books I have acquired. Please keep it coming.
-JRV
Posted by: John R. Vokey | September 15, 2009 at 20:40
Thanks John! I really appreciate the kind words.
On Tue, Sep 15, 2009 at 8:40 PM, wrote:
Posted by: David Smith | September 16, 2009 at 10:30