Tools to generate complex heatmaps recommendations

Question

[ddh8602]

Hi I need to create a complex heatmap of presence/absence of antibiotic resistance genes, abundance, phylogeny and drug classes like the ones on the image attached (sorry for the quality, source: sraX). I would appreciate if someone could recommend me a free web page or a tool I can use to create them. I have used seaborn and matplotlib before to create heatmaps but I don´t really know if I can make them that complex and integrate more than one chart using that packages.

[bioinformatics2020]

Your image isn't showing.

[ddh8602]

Link to the image: https://www.dropbox.com/s/bjvbzkcbo52qmk1/heatmap%20complex.PNG?dl=0 (don´t know why it isn´t working)

[Ram]

Please see How to add images to a Biostars post to add your images properly - we recommend imgbb as an image hosting service, as it seems to work all over the world and doesn't need a user account to be created.

Answer 1

[Ram]

The R package ComplexHeatmap is the best heatmap building software I've ever encountered. It is packed with customization options and the developer helps you out with custom features, so that's the software I'd use.

[bioinformatics2020]

Agreed (if the OP is okay with running this in R.) I started out with pretty heatmap (which might be easier for OP to use), but came to Complex once I needed more customizations. I've never looked back.

[Ram]

Indeed. I personally avoid pheatmap and heatmap.2 because they are not as structured as CH. I love how we can Heatmap(...) %v% Heatmap(...) in CH.