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

Question

[WUSCHEL]

**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?

[zx8754]

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

Answer 1

[manuel.belmadani]

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:

> 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().

[cpad0112]

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"