How to create a Venn diagram using ortholog clusters?

Question

[fhsantanna]

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.

Answer 1

[Deepak Tanwar]

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

[Deepak Tanwar]

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

[fhsantanna]

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).

[bioinfool]

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