[SciPy-user] "clustergrams"/hierarchical clustering heat maps

Zachary Pincus zachary.pincus@yale....
Tue Feb 3 08:43:26 CST 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.)


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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