Question

Venndigram of LIMMA decideTests() function for more than 5 sets

0

Entering edit mode

Seymoo • 0

@seymoo-12522

Last seen 10 weeks ago

Oslo

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 • 2.3k views

ADD COMMENT • link updated 7.0 years ago by Gordon Smyth 51k • written 7.0 years ago by Seymoo • 0

score 1 · Answer 1 · 2017-11-03

1

Entering edit mode

Aaron Lun ★ 28k

@alun

Last seen 1 hour ago

The city by the bay

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 COMMENT • link 7.0 years ago Aaron Lun ★ 28k

0

Entering edit mode

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

ADD REPLY • link 7.0 years ago Seymoo • 0

0

Entering edit mode

Hi I am trying to do the same thing and as advised tried to use the vennCounts output in UpSet function I am getting an error saying :

Error in colSums(data[sets]) : 'x' must be an array of at least two dimensions

I checked some examples and in all they use a dataframe as an input I cannot find a way to convert class ‘"VennCounts"’ to a data.frame

Could you please explain how do I use the vennCounts output? Thanks

ADD REPLY • link 4.1 years ago mila.grinblat • 0

score 0 · Answer 2 · 2017-11-03

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.