Hierarchical Clustering using both rows and columns

Question

[gs000095]

Hello,

I have data with genes as row names and their respective expression levels in different samples. Samples are column names.

I want to perform hierarchical clustering, however, I would like to cluster using both genes and samples ie. rows and columns as when I use either rows or columns the result is not as I expect it to be. I am trying to recreate the results we got using MeV (Multiple experiment viewer) wherein we had selected both genes and samples for building the tree.

Can anyone suggest any good packages in R/ Python wherein I can perform this?

Thank you for any help in advance.

[gs000095]

Thank you so much for your suggestions, I will take a look at these.

Answer 1

[Asaf]

heatmap.2 from gplots can do this in R. I also heard some good things about ComplexHeatmap: https://jokergoo.github.io/ComplexHeatmap-reference/book/a-single-heatmap.html#get-orders-and-dendrograms-from-heatmap

Answer 2

[jared.andrews07]

pheatmap is also an easy/popular option for this.