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Question: Venndigram of LIMMA decideTests() function for more than 5 sets
0
gravatar for Seymoo
20 days 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 19 days ago by Gordon Smyth32k • written 20 days ago by Seymoo0
1
gravatar for Aaron Lun
19 days ago by
Aaron Lun17k
Cambridge, United Kingdom
Aaron Lun17k 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 19 days ago • written 19 days ago by Aaron Lun17k

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

ADD REPLYlink written 18 days ago by Seymoo0
0
gravatar for Gordon Smyth
19 days 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 17 days ago • written 19 days ago by Gordon Smyth32k
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