Hierarchical Clustering, Cluster Heat Maps In Java

Question

[Sashi Kiran Challa]

Hello all,

I am new to this forum and I am glad I found one in Bioinformatics too. I hope I can ask this question here.

Has anyone been able to generate cluster heatmaps using any library in Java ?

I recently got to learn that heatmaps are different from cluster heat maps in just that in the cluster heatmaps there are dendrograms for both genes as well as samples. So essentially Hierarchical clustering (thats what I am working on) is to be performed once on the genes and once on the samples.

I was looking at JFreechart, JTreeview. In JFreechart I did not find any method to directly get a cluster heat map. And with JTreeview, it needs 3 input files in particular format like the .CDT file, .gtr file, .atr file. I am curious to know if there is any other direct way to generate these cluster heat maps.

Please enlighten me

Thanks in advance

Answer 1

[Istvan Albert]

I know that the Multiexperiment Viewer suite is written in Java.

While it is not usually used as a library I think you might be able to import some of its internals in your own code. It is worth a try, as you could get access to numerous other tools as well.

[Sashi Kiran Challa]

Thanks Istvan. will look at this.

Answer 2

[Jeroen Van Goey]

GenePilot™ is a Java-based Analysis suite, which provides a MicroArray Analysis capabilities.

You can export your results as Cluster Heatmaps. They give the following example of a local heatmap of the currently selected cluster along with the top dendigram (if applicable), column information, average thumbnail, row info and Gene Ontology Information (if applicable):

[Sashi Kiran Challa]

Thank you for making me aware of this. I was interested in knowing if I could use any libraries in Java that have HC already implemented as a method which I could use with the clusters I get and plot them as a cluster heatmap.

[Sashi Kiran Challa]

Thank you, I didnt know about this. I was actually more interested in knowing if any libraries in Java already have this method of generating cluster heat maps implemented, which I could use with the clusters that I generate.