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Is there any Library in Java that has Cluster Heat Maps already implemented ? Can I use that Library in my code to generate a cluster heat map ? I am looking to plot cluster heat maps from gene expression data that I have.

+1  A: 

Can you leverage off Java TreeView (overview here) ? Although it's a standalone app, I'd hope you can create a suitable library from it.

Brian Agnew
+1  A: 

How about Java Treeview - "An Open Source, Extensible Viewer for Microarray Data in the PCL or CDT format"

You can try sample applets online: http://jtreeview.sourceforge.net/examples/applets.html

f3lix