Question: How to draw a phylogenetic tree together with a genome locus structure?
2
gravatar for vanya.antonov
19 months ago by
Moscow, Russia
vanya.antonov30 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 • 1.1k views
ADD COMMENTlink modified 18 months ago by Guangchuang Yu1.8k • written 19 months ago by vanya.antonov30
2
gravatar for WouterDeCoster
19 months ago by
Belgium
WouterDeCoster28k 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 19 months ago by WouterDeCoster28k
4
gravatar for Guangchuang Yu
19 months ago by
Guangchuang Yu1.8k
China/Hong Kong/The University of Hong Kong
Guangchuang Yu1.8k 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 19 months ago by Guangchuang Yu1.8k
3
gravatar for george.ry
19 months 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 19 months ago by george.ry1.1k
2
gravatar for Brice Sarver
19 months ago by
Brice Sarver2.4k
United States
Brice Sarver2.4k 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 19 months ago • written 19 months ago by Brice Sarver2.4k

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

Ivan

ADD REPLYlink written 19 months ago by vanya.antonov30
1
gravatar for Guangchuang Yu
18 months ago by
Guangchuang Yu1.8k
China/Hong Kong/The University of Hong Kong
Guangchuang Yu1.8k wrote:

Now it is supported by ggtree.

ADD COMMENTlink written 18 months ago by Guangchuang Yu1.8k
0
gravatar for Erik Wright
19 months ago by
Erik Wright350
Erik Wright350 wrote:

You might take a look at facet_plot.

ADD COMMENTlink written 19 months ago by Erik Wright350
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 698 users visited in the last hour