[SciPy-user] "clustergrams"/hierarchical clustering heat maps
Zachary Pincus
zachary.pincus at yale.edu
Tue Feb 3 09:43:26 EST 2009
Hi David,
I don't know about making heat-maps in Python, but what I recently
used for the task was the combination of "Cluster 3" (an update of
Mike Eisen's original hierarchical-clustering-for-microarrays tool) to
do the clustering, and "Java TreeView" to draw the heatmap/dendrogram.
Cluster 3 is a bit annoying to one used to scripting analyses (lots of
GUI button-pressing), but there's also a python library. Or you could
just scrutinize the output format (it barfs out a few text files) and
use your own clustering tools. TreeView then accepts these text files
and lets you manipulate the heatmap / dendrograms (e.g. flipping nodes
to get visually better results). You can then export to PS or other
formats. (The PS output is pretty clean, so you can edit in
Illustrator or whatnot easily.)
Zach
On Feb 3, 2009, at 2:12 AM, David Warde-Farley wrote:
> Hi all,
>
> I was recently asked to cluster some data and I know from experience
> that people use these heat maps to look for patterns in multivariate
> data, often with a dendrogram off to the side. This involves sorting
> the rows and columns in a certain fashion, the details of which are
> somewhat fuzzy to me (and, truthfully, I'm happy with it staying that
> way for now).
>
> I notice that dendrogram plotting is available in
> scipy.cluster.hierarchy, and was wondering if the something for
> producing the associated sorted heat maps is available anywhere
> (within SciPy or otherwise).
>
> Many thanks,
>
> David
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