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!

use this instead:

    library(gplots)

  x <- list(
    `set 1` = c("A","B","C","D"),
    `set 2` = c("A","C","E","F"),
    `set 3` = c("A","D","F","G")
      )   

    v.table <- venn(x)

    print(v.table)

    all_intersections <- attr(v.table, "intersections")
    for (comparison in names(all_intersections)) {
      cat(comparison, "\n")
      print(all_intersections[[comparison]])
    }

I think intersect() is exactly what you need

intersect(UPDEGsTR40SR40genes, intersect(UPDEGsTRRSRRgenes, UPDEGsTR120SR120genes))