How to annotate nodes in trees using R?

Question

[Speed.Lee]

Hi, I am a newbie in biology. Currently, I am working with R to generate trees (but not in biology, for other subjects). I just have some concern using phangron and ape (other packages of R is OK if they can solve this problem).

My data is like this, binary datasets.

And what I want to generate are trees like this: all the characteristics made the difference are labelled in the tree (automatically, not point by me after generated the tree). I do not mind if they are annotated at nodes or on edges.

Is it possible? How can I do it? Thanks in advance for the comments.

Answer 1

[Bioinformatics_NewComer]

Check itol's website. Also, see http://docs.phylotoast.org/en/latest/scripts/iTol.html

[Speed.Lee]

Thanks, this is a great website, but I am afraid it is not so suitable for me because I need to finish it by R.

I found Last common ancestor method mentioned on the website might be helpful for this topic, so I decide to do some research on it. Thanks again for the help!

[Bioinformatics_NewComer]

Try - ggtree and phyloseq packages