vennDigram for multiple RNA-seq data

Question

[ta_awwad]

Hello everybody, I have 30 RNA-seq data sets (4 conditions plus my control) and I ran Deseq2 pipeline to analyse them. now I would like to intersect all these data in a form of VennDiagrams. is there any package or simple code which does that. I would like to have total genes overlap, unregulated and down regulated genes in one panel.

could you please help thanks

Answer 1

[andrew.j.skelton73]

Venn diagrams suck to interpret and they do not scale well. At all. Just look at the example that @e.rempel posted, it's not intuitive to get the information you want quickly, and making it proportional will skew the reader's view of the data further. I'd strongly recommend Upset Plots, which are available in Github or CRAN. They're far easier to look at and scale much better.

[e.rempel]

I agree that the interpreting of 5-way Venn Diagram is not easy.

[ivivek_ngs]

+1 for UpsetR, there is also jvenn if one would like to try for 6 way Venn diagram, only good when you have gene lists or stuffs but I would still make use of upsetR as for data science and analytics it is much a better resource.

Answer 2

[vmicrobio]

there is a R package : 'VennDiagram'

also you can do it very easily using venny

Answer 3

[e.rempel]

R-package SystemPiper offers the possibility to Plot 2-5 way Venn diagrams. E.g.

The manual is available on here

[ta_awwad]

thanks but I don't know how to make it proportional.

[e.rempel]

I am not sure whether plotting proportional 5-way Venn Diagram is even (mathematically) possible. You could also try a shiny app for plotting of Venn Diagrams.