How to draw a phylogenetic tree together with a genome locus structure?
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5.9 years ago
ivan.antonov ▴ 90

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

enter image description here

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

tree draw tool • 2.9k views
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5.9 years ago
Guangchuang Yu ★ 2.5k

Now it is supported by ggtree.

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5.9 years ago
Guangchuang Yu ★ 2.5k

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 :).

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5.9 years ago
george.ry ★ 1.2k

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

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5.9 years ago
Brice Sarver ★ 3.7k

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.

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

Ivan

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5.9 years ago

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

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5.9 years ago
Erik Wright ▴ 410

You might take a look at facet_plot.

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