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Question: Venndigram of LIMMA decideTests() function for more than 5 sets
0
gravatar for Seymoo
12 months ago by
Seymoo0
Oslo
Seymoo0 wrote:

I'd like to make Venn diagram from Limma `decideTests` results. Limma `vennDiagram` function is limited to maximum of 5 sets. I tried to make the plot using `veneluer` and 'vennerable` packages in R but I was not successful.

appreciate if someone could help me with this issue.

Thanks a lot!

ADD COMMENTlink modified 12 months ago by Gordon Smyth35k • written 12 months ago by Seymoo0
1
gravatar for Aaron Lun
12 months ago by
Aaron Lun21k
Cambridge, United Kingdom
Aaron Lun21k wrote:

More than 5 sets... and you expect the plot to be interpretable by mere humans? I would suggest using the output of vennCounts to create UpSet plots instead (https://cran.r-project.org/package=UpSetR).

ADD COMMENTlink modified 12 months ago • written 12 months ago by Aaron Lun21k

Thanks for your suggestion Aaron, I will look in that.

ADD REPLYlink written 12 months ago by Seymoo0
0
gravatar for Gordon Smyth
12 months ago by
Gordon Smyth35k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth35k wrote:

I don't have any plans to offer Venn diagrams in limma for more than 5 sets, because I don't find Venn diagrams with more than 5 sets to be at all useful. They seem far too contrived to help with interpretation. With so many sets, just looking at the tabular output from vennCounts() is better. Alternatively you could try Aaron's suggestion of the UpSetR package, which produces what is essentially a pictorial representation of the vennCounts table.

ADD COMMENTlink modified 12 months ago • written 12 months ago by Gordon Smyth35k
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