I plotted my genelists using the VennDiagram R package, and the diagram looks fine.
Try this:
library(VennDiagram)
draw.triple.venn(65, 75, 85, 35, 15, 25, 5, c("First", "Second", "Third"))
Or this for a nicer view, and 4 groups:
A <- sample(1:1000, 400, replace = FALSE);
B <- sample(1:1000, 600, replace = FALSE);
C <- sample(1:1000, 350, replace = FALSE);
D <- sample(1:1000, 550, replace = FALSE);
E <- sample(1:1000, 375, replace = FALSE);
venn.diagram(x = list(A = A,D = D,B = B,C = C), filename = "Venn.tiff",
col = "transparent", fill = c("cornflowerblue","green","yellow","darkorchid1"),
alpha = 0.50, label.col = c("orange", "white", "darkorchid4", "white", "white",
"white", "white", "white", "darkblue", "white", "white", "white", "white",
"darkgreen", "white"), cex = 1.5, fontfamily = "serif", fontface = "bold",
cat.col = c("darkblue", "darkgreen", "orange", "darkorchid4"), cat.cex = 1.5,
cat.pos = 0, cat.dist = 0.07, cat.fontfamily = "serif", rotation.degree = 270,
margin = 0.2)
There are plenty of more examples in the VennDiagram Document (Here)