Question: How to create a Venn diagram using ortholog clusters?
0
gravatar for fhsantanna
5.8 years ago by
fhsantanna490
Brazil
fhsantanna490 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.

ADD COMMENTlink modified 5.8 years ago by Deepak Tanwar4.1k • written 5.8 years ago by fhsantanna490
2
gravatar for Deepak Tanwar
5.8 years ago by
Deepak Tanwar4.1k
ETH Zürich, Switzerland
Deepak Tanwar4.1k 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 COMMENTlink written 5.8 years ago by Deepak Tanwar4.1k
1

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

ADD REPLYlink written 5.8 years ago by Deepak Tanwar4.1k

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 REPLYlink modified 5.7 years ago • written 5.7 years ago by fhsantanna490

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 REPLYlink written 10 months ago by bioinfool20
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