Hello everyone!
I have a question on heatmaps with a cladogram (like the one shown in the picture, taken from https://blog.bioturing.com/2018/05/08/how-to-build-a-hierarchical-clustering-heatmap-with-biovinci/ )
The sort of diagram i want to make is slightly different:
1) in the columns, i want to display isolated (non-related) proteins or functions (so, i will not have anything that could resemble distances for making [the upper] cladogram)
2) Usually for the rows representative species are chosen, however is it possible to present higher taxa? Apparently, not all species within the selected taxa will have the proteins/functions that will be presented in the columns. How to best select taxa in this case? (i may have taxa, however, i may not necessarily have distances between them. If distances are absolutely required — from where can i obtain them?)
3) In which program and how to create such a heatmap?
The purpose of this diagram is trying to identify for which clades/organisms particular functions/functional proteins are proper.
Thank you for any insight and have a nice day!
Muchas gracias, Otoniel!! It looks to be the procedure I am looking for!
Just to be sure — isn't it necessary to specify phylogenetic distances to draw the dendrograms (is for this the "scale = "none"" option)? Most cladogram-drawing programs I have saw asked for them and for my purpose denoting the simple kinship would be more than enough.
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