Question: Some script or program to create venn diagrams for Orthofinder results?
gravatar for imda
23 months ago by
imda10 wrote:

Some script or program to create venn diagrams for Orthofinder results? or maybe a Rscript? To be honest I am a begginer in R

ADD COMMENTlink modified 23 months ago by Philipp Bayer6.9k • written 23 months ago by imda10

Have you seen this post? Programme/Script For Venn Daigram -

it's a collection of three other posts, repeated below.

Try to search the site by yourself first, there are a lot of similar posts here.

Some others, already mentioned above:


A: Tool To Generate Proportional Venn Diagrams?

Venn/Euler Diagram Of Four Or More Sets

Venndiagram Using R


What kind of data do you have? See the right panel, there are a lot of

different posts for Venn-diagrams.

Creating a Venn Diagram from Microarray Data

Extracting Gene Names From Venn Diagram

Venn diagram with 11 sets

Venn diagram for annotation results

Venn diagrams for multiple (8) data lists in R

Using Genes List From Limma Venn Diagram To Make Heat Map

Need help with creating a Euler diagram from a csv file

Venn diagram in R - there is a large post-collection inside,

as well as R packages you could use.

Draw Diagrams For Intersection Between Many Sets - again there are a lot of links inside.

A lot depend upon your data, more details are needed.

ADD REPLYlink modified 23 months ago • written 23 months ago by natasha.sernova3.8k
gravatar for Philipp Bayer
23 months ago by
Philipp Bayer6.9k
Philipp Bayer6.9k wrote:

A while ago I wrote a script and put it onto GitHub - it's for OrthoMCL output but as far as I remember the Orthofinder Orthogroups.txt file tries to mimic OrthoMCL output

Of course, with more than three sets a Venn diagram becomes messy. In that case I'd go for Upset-plots, my script puts out the table of gene and cluster overlaps which you should be able to put into UpSetR.

ADD COMMENTlink written 23 months ago by Philipp Bayer6.9k

Thanks for the answer, I am trying to run your script. However, I do not find outputs such as singletons.txt and families.txt in Orthofinder, do you know if Orthofinder has a similar result?



ADD REPLYlink written 23 months ago by imda10

Hi Ivan

the families.txt file you can write yourself, have a look at the example families.txt in the repository's README, or in the example_data folder. For the singletons file, that's just a list of unclustered genes:

These gene names are in the Orthogroups_UnassignedGenes.tsv table, just slightly different, since it's a proper table with several columns... I guess you could reformat that table? I just remembered that OrthoMCL distinguishes species names using the | between species name and gene name, so you'd have to add that too

ADD REPLYlink written 23 months ago by Philipp Bayer6.9k

For the singletons file I l obtained this file Orthogroups_UnassignedGenes.csv but it does not have the format for your program. Any idea how to re format it?

OG0046733 Sopen07g010930.1 OG0046734 Sopen07g010940.1

For families.txt I got the file Orthogroups.GeneCount.csv, which is: Datura_stramonium_Teo1 Datura_stramonium_Tic23 Solanum_lycopersicum Solanum_pennellii Solanum_pimpinellifolium Solanum_tuberosum Total OG0000000 21 36 59 79 6 51 252 OG0000001 2 1 0 57 96 1 157 OG0000002 3 1 21 99 3 14 141

I do not know if I have to transpose this table?

and finally, I do not know if the output from OrtoMCL --> groups.txt is similar to the output from Orthofinder (two tab columns)

OG0000000: Datura_stramonium10788-RA Datura_stramonium11774-RA Datura_stramonium12237-RA Datura_stramonium12349-RA Datura_stramonium13941-RA Datura_stramonium14119-RA Datura_str$ OG0000001: Datura_stramonium27885-RA Datura_stramonium_Teo22898-RA Datura_stramonium_Teo27500-RA SPi07005.1 SPi12091.1 SPi12112.1 SPi12556.1 SPi12807.1 SPi14172.1 SPi14174.1 SPi

ADD REPLYlink written 23 months ago by imda10
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