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Question: Venndigram of LIMMA decideTests() function for more than 5 sets
0
gravatar for Seymoo
3 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 3 months ago by Gordon Smyth32k • written 3 months ago by Seymoo0
1
gravatar for Aaron Lun
3 months ago by
Aaron Lun18k
Cambridge, United Kingdom
Aaron Lun18k 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 3 months ago • written 3 months ago by Aaron Lun18k

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

ADD REPLYlink written 3 months ago by Seymoo0
0
gravatar for Gordon Smyth
3 months ago by
Gordon Smyth32k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth32k 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 3 months ago • written 3 months ago by Gordon Smyth32k
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