How to draw a phylogenetic tree together with a genome locus structure?

Question

[ivan.antonov]

Hello, I am wondering, what tool/R-package can be used to draw this type of tree (preferably, programmatically)?

The image is taken from: https://www.ncbi.nlm.nih.gov/pubmed/26773003

Answer 1

[Guangchuang Yu]

Now it is supported by ggtree.

Answer 2

[Guangchuang Yu]

ggtree with ggbio can do this. It needs some hack currently.

I will contact the author of ggbio to work out a way more user friendly :).

Answer 3

[george.ry]

If you're handy with Python, then ETE Toolkit will do this and more.

Answer 4

[Brice Sarver]

You asked a similar question last week (https://www.biostars.org/p/217510/#217564), and my answer is the same. This looks to be a case of two different graphics combined. Check the differences in the fonts, for example.

[ivan.antonov]

Yes, Brice -- nice note about the font! Thank you once again for the answer:)

Ivan

Answer 5

[WouterDeCoster]

The left part looks rather standard so no need for recommendations there, probably something like the right part could be made with https://github.com/griffithlab/GenVisR

Answer 6

[Erik Wright]

You might take a look at facet_plot.