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vennDigram for multiple RNA-seq data

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

rna-seq deseq2 r
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updated by andrew.j.skelton73 andrew.j.skelton73 • written by ta_awwad ta_awwad

3 answers

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.

enter image description here

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written by andrew.j.skelton73 andrew.j.skelton73

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

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written by e.rempel e.rempel

+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.

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written by ivivek_ngs ivivek_ngs

there is a R package : 'VennDiagram'

also you can do it very easily using venny

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written by vmicrobio vmicrobio

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

VennDiagram

The manual is available on here

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written by e.rempel e.rempel

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

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written by ta_awwad ta_awwad

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.

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written by e.rempel e.rempel

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