Extract Genes from ggvenn

Question

[axe880]

Hi there,

Here is my script for generating a Venn diagram:

vennlistUp <- list( "Control" = UPDEGsTRCSRCgenes,
                    "40-min" = UPDEGsTR40SR40genes,
                    "120-min" = UPDEGsTR120SR120genes,
                    "Recovery" = UPDEGsTRRSRRgenes)

vennlistUp_venn <- ggvenn(vennlistUp, fill_color = c("orange", "#0073C2FF", "#EFC000FF", "#868686FF"), 
                      stroke_size = 1, set_name_size = 8, text_size = 5)
vennlistUp_venn*

This works well and shows what I want it to.

My issue is, I need to extract the gene ID's that are shared across three time points: 40-min, 120-min, and Recovery. I do not want to observe the genes that overlap with the control.

Is there a method of doing this? I understand the intersect function can intersect the genes, but I seem to only be able to do this for all 4 time points at once.

Any help is appreciated, thanks!

Answer 1

[Michael]

intersect(intersect(UPDEGsTRRSRRgenes, UPDEGsTR120SR120genes), UPDEGsTR40SR40genes)

This should do it.

[axe880]

Thank you but I think I tried this to no avail. If I show you my diagram:

I am trying to look at the 89 genes. This is because there is no overlap with the control. When I tried the suggested command, I instead got a number which included both the 89 and the 627, where 627 is the genes seen across all 4 points.

So, in theory, my problem is my inability to remove the 627 genes from the 89.

Is there any solution you could perhaps suggest for this?

Thanks again.

[Michael]

So you want the intersection of 40min,120min, Recovery, but not those genes that are also in the control? I might have overread this, but set operators in R are very powerful, so:

 setdiff (intersect(intersect(UPDEGsTRRSRRgenes, UPDEGsTR120SR120genes), UPDEGsTR40SR40genes),  UPDEGsTRCSRCgenes)

will remove the control genes from the intersection. Hope this works out

[axe880]

Worked perfect - appreciate the help.