Question: How to draw a phylogenetic tree together with a genome locus structure?
2
gravatar for ivan.antonov
2.9 years ago by
ivan.antonov80
Moscow, Russia
ivan.antonov80 wrote:

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

tool tree draw • 1.8k views
ADD COMMENTlink modified 2.8 years ago by Guangchuang Yu2.2k • written 2.9 years ago by ivan.antonov80
3
gravatar for Guangchuang Yu
2.8 years ago by
Guangchuang Yu2.2k
China/Guangzhou/Southern Medical University
Guangchuang Yu2.2k wrote:

Now it is supported by ggtree.

ADD COMMENTlink written 2.8 years ago by Guangchuang Yu2.2k
4
gravatar for Guangchuang Yu
2.9 years ago by
Guangchuang Yu2.2k
China/Guangzhou/Southern Medical University
Guangchuang Yu2.2k wrote:

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 :).

ADD COMMENTlink written 2.9 years ago by Guangchuang Yu2.2k
3
gravatar for george.ry
2.9 years ago by
george.ry1.1k
United Kingdom
george.ry1.1k wrote:

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

ADD COMMENTlink written 2.9 years ago by george.ry1.1k
2
gravatar for Brice Sarver
2.9 years ago by
Brice Sarver2.9k
United States
Brice Sarver2.9k wrote:

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.

ADD COMMENTlink modified 2.9 years ago • written 2.9 years ago by Brice Sarver2.9k

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

Ivan

ADD REPLYlink written 2.9 years ago by ivan.antonov80
1
gravatar for WouterDeCoster
2.9 years ago by
Belgium
WouterDeCoster40k wrote:

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

ADD COMMENTlink written 2.9 years ago by WouterDeCoster40k
0
gravatar for Erik Wright
2.9 years ago by
Erik Wright360
Erik Wright360 wrote:

You might take a look at facet_plot.

ADD COMMENTlink written 2.9 years ago by Erik Wright360
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