How Can I Create A Heat Map With Phylogeny In R?

Question

[microbeatic]

I am trying to create a heat map of presence and absence of set of genes in number of organisms. I am using pheatmap, which i think is a fabulous package, if i just want a heat map. But, it doesn't have any options to integrate phylogenetic information. Likewise, i looked into some other R packages that either deals with phylogenetic or heat map, but most of these tools were exclusive at what they do, meaning, phylogenetic packages didn't do well with heat maps and vice versa.

I have looked in to these two posts 1 and 2, but they both recommend iTol at the end, which is a fascinating tool, but doesn't have all the functionality a heat map package in R has.

Are there any packages that i am missing?

[Michael]

Can you convert your tree into a dendrogram and simply use heatmap.2 (is it rooted)? I guess in the standard setting the row-side tree is a bit narrow, but the width could be increased. Did you look into package ape? I guess the point is defining how the plot should look, and then pick one tool that is close and possibly modify it.

[Astoulpho]

you already have the topography, right?you have to make the topography as a 'dist' objetct and pass this object to the heatmap function

Answer 1

[ofanoyi]

Check this post: http://www.polarmicrobes.org/?p=562