Question: Venndigram of LIMMA decideTests() function for more than 5 sets
0
23 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!

limma venn diagram vennplot • 443 views
modified 23 months ago by Gordon Smyth38k • written 23 months ago by Seymoo0
Answer: Venndigram of LIMMA decideTests() function for more than 5 sets
1
23 months ago by
Aaron Lun25k
Cambridge, United Kingdom
Aaron Lun25k 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).

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

Answer: Venndigram of LIMMA decideTests() function for more than 5 sets
0
23 months ago by
Gordon Smyth38k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth38k 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.