Question: How to draw a phylogenetic tree together with a genome locus structure?
2
gravatar for vanya.antonov
7 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 • 570 views
ADD COMMENTlink modified 6 months ago by Guangchuang Yu1.4k • written 7 months ago by vanya.antonov30
2
gravatar for WouterDeCoster
7 months ago by
Belgium
WouterDeCoster17k 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 7 months ago by WouterDeCoster17k
3
gravatar for Guangchuang Yu
7 months ago by
Guangchuang Yu1.4k
China/Hong Kong/The University of Hong Kong
Guangchuang Yu1.4k 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 7 months ago by Guangchuang Yu1.4k
3
gravatar for george.ry
6 months ago by
george.ry970
United Kingdom
george.ry970 wrote:

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

ADD COMMENTlink written 6 months ago by george.ry970
2
gravatar for Brice Sarver
7 months ago by
Brice Sarver2.3k
United States
Brice Sarver2.3k 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 7 months ago • written 7 months ago by Brice Sarver2.3k

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

Ivan

ADD REPLYlink written 7 months ago by vanya.antonov30
1
gravatar for Guangchuang Yu
6 months ago by
Guangchuang Yu1.4k
China/Hong Kong/The University of Hong Kong
Guangchuang Yu1.4k wrote:

Now it is supported by ggtree.

ADD COMMENTlink written 6 months ago by Guangchuang Yu1.4k
0
gravatar for Erik Wright
6 months ago by
Erik Wright320
Erik Wright320 wrote:

You might take a look at facet_plot.

ADD COMMENTlink written 6 months ago by Erik Wright320
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