How to get the list of common genes from a VennDiagram?

**Package ‘![VennDiagram][1]’.** How can I get the list of common objects in each combination?

For e.g. what are the common 44 Genes in interset (similar image got from online)?

I have used below scripts

Overlap <- calculate.overlap(x = list(BB, BB, BRR))

Overlap[[1]]

But in this method, I can not find the list of 1761, 466 genes

how these numbers are given?

Even when I tried Overlap$a5 , Overlap$a7, etc this also not given some of the values correctly?

Could someone help me?

rna-seq r

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updated 6.6 years ago by mbelmadani

• written 6.6 years ago by WUSCHEL

Provide example data, calculate.overlap does exactly what you need, try the examples from the manuals. Also, why BB is repeated twice?

If you need just the overlap of genes from 3 sets, try:

intersect(intersect(1:4, 2:5), 3:7)
# [1] 3 4

Or more generic solution:

Reduce(intersect, list(1:4, 2:5, 3:7))
# [1] 3 4

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written 6.6 years ago by zx8754

1 answer

From what I can tell, the as are distributed from top left to right, to bottom. i.e. a1 = 1761 a2=126 a3=466 a4=64 a5=44 a6=27 a7=366

This is based on: enter image description here

> library("VennDiagram")
> 
> gene_list = paste0("GENE", 1:1000)
> 
> studies = list( S1=sample(gene_list, 700, replace = FALSE),
+                 S2=sample(gene_list, 700, replace = FALSE),
+                 S3=sample(gene_list, 700, replace = FALSE) )
> 
> ol = calculate.overlap(x = studies)
> ol_size=sapply(ol, length)
> 
> 
> venn.diagram(
+   x = studies,
+   euler.d = TRUE,
+   filename = "Euler_3set_scaled.tiff",
+   cex = 2.5,
+   cat.cex = 2.5,
+   cat.pos = 0
+ );
[1] 1
> # Get the 63
> length( setdiff(studies$S1, union(studies$S2, studies$S3)) )
[1] 63
> # Confirm order
> ol_size
 a5  a2  a4  a6  a1  a3  a7 
351 143 143 134  63  72  72

And it matches the order from a1 to a7 going left-right, top-bottom.

If you want to be sure of what you're getting, you can use set operators like I did with setdiff() and union().

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written 6.6 years ago by mbelmadani

Probably, this is another way:

t=get.venn.partitions(studies, keep.elements = T, force.unique = T)
t$..values..[1] # To get all common genes
t$..set..
[1] "S1∩S2∩S3"     "(S2∩S3)∖(S1)" "(S1∩S3)∖(S2)" "(S3)∖(S1∪S2)"
[5] "(S1∩S2)∖(S3)" "(S2)∖(S1∪S3)" "(S1)∖(S2∪S3)"

 ol_size
 a5  a2  a4  a6  a1  a3  a7 
338 148 154 145  60  69  63 
 lengths(t$..values..[1])
  1 
338

OP can edit this code for better. Remove lengths to print the gene list:

> for (length in (1:length(t$..set..))) {
+     print (paste(t$..set..[length], lengths(t$..values..[length])), sep="\t")
+ }
[1] "S1∩S2∩S3 338"
[1] "(S2∩S3)∖(S1) 145"
[1] "(S1∩S3)∖(S2) 154"
[1] "(S3)∖(S1∪S2) 63"
[1] "(S1∩S2)∖(S3) 148"
[1] "(S2)∖(S1∪S3) 69"
[1] "(S1)∖(S2∪S3) 60"

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written 6.6 years ago by cpad0112