Question: Some script or program to create venn diagrams for Orthofinder results?
0
gravatar for imda
6 months ago by
imda10
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 6 months ago by Philipp Bayer6.4k • written 6 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:

<h6>#</h6>

A: Tool To Generate Proportional Venn Diagrams?

Venn/Euler Diagram Of Four Or More Sets

Venndiagram Using R

<h6>#</h6>

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 6 months ago • written 6 months ago by natasha.sernova3.5k
1
gravatar for Philipp Bayer
6 months ago by
Philipp Bayer6.4k
Australia/Perth/UWA
Philipp Bayer6.4k 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

https://github.com/philippbayer/orthomclToVenn

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 6 months ago by Philipp Bayer6.4k

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?

Best

Ivan

ADD REPLYlink written 6 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: https://github.com/philippbayer/orthomclToVenn/blob/master/example_data/singletons.txt

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 5 months ago by Philipp Bayer6.4k

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 5 months ago by imda10
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