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How To Find And Display Biclusterings For Gene Expression From R Or Python?

What are some available packages in either Python or R for creating biclustering heatmaps with dendrograms for gene expression value (e.g., from RNASEQ), as in this figure?

http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002936#pcbi-1002936-g003

the clustering is done across two dimensions (rows and columns), displayed as as a heat map with dendrograms for both axes.

r heatmap genomics clustering python
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updated by Ram Ram • written by user user

This is possibly a duplicate of several heatmap related questions, see: heatmap in R the heatmap type of functions are all biclustering cabable by default: How do I make a heatmap in R?, Clustering data (RNA-seq) using R to produce a heatmap, How do I draw a heatmap in R with both a color key and multiple color side bars?, Heatmap visualisations?, How to draw a csv data file as a heatmap using numpy and matplotlib, etc. etc. etc. In fact there are so many related questions that it seems very hard to justify to keep another one open. Please tell me, if that settles your claim.

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written by Michael Dondrup Michael Dondrup

No. This is not a simple how to draw a heatmap. It's a biclustering which is a statistical procedure, whose output happens to be visualized as a heatmap with two dendrograms, along each side. It's not the same as these simple how to make a heatmap questions at all. It requires clustering wrt two dimensions and then appropriate dendrogram visualization

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written by user user

But that is nothing special, all R solutions mentioned above do biclustering by default.

• 284 views • link
written by Michael Dondrup Michael Dondrup

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