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Question: How to create a Venn diagram using ortholog clusters?
0
gravatar for fhsantanna
5.8 years ago by
fhsantanna • 490
Brazil
fhsantanna • 490 wrote:

Hi.

I have utilized the software get_homologues in order to find ortholog clusters of 4 bacterial strains.

I have obtained a huge table file with the following format:

Strains Group 1 Group 2 Group 3 Group 4 Group 5
Organism_A 1 1 1 1 3
Organism_B 1 1 1 1 0
Organism_C 1 1 1 1 1
Organism_D 1 1 1 1 1

 

Do you know a venn plotter software that is able to read this kind of table?

Thanks.
ortholog venn diagram get_homologues • 3.4k views
ADD COMMENT • link •
modified 5.8 years ago by Deepak Tanwar • 4.1k • written 5.8 years ago by fhsantanna • 490
2
gravatar for Deepak Tanwar
5.8 years ago by
Deepak Tanwar • 4.1k
ETH Zürich, Switzerland
Deepak Tanwar • 4.1k wrote:

You could try the VennDiagram package.

R (CRAN)

Have a look at its documentation and examples, to see how it works.

Here is an example: http://rstudio-pubs-static.s3.amazonaws.com/13301_6641d73cfac741a59c0a851feb99e98b.html
ADD COMMENT • link written 5.8 years ago by Deepak Tanwar • 4.1k
1

Also, havea look at http://www.ats.ucla.edu/stat/r/faq/venn.htm

ADD REPLY • link written 5.8 years ago by Deepak Tanwar • 4.1k

Thank you. I managed doing it filtering the gene groups using awk. After I utilized the gene group lists in Jvenn (http://bioinfo.genotoul.fr/jvenn/example.html).

ADD REPLY • link modified 5.7 years ago • written 5.7 years ago by fhsantanna • 490

Hello fhsantanna, i wonder if you can still remember the awk script that you used for the filtering of the orthomcl report and care to share to me? Thanks

ADD REPLY • link written 10 months ago by bioinfool • 20
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