Venn diagrams is commonly used to visualize the overlapping among data sets, including differential gene expression data under various condition. Here I shaw you one way to draw venn diagram (see below) in R using VennDiagram package using data generated from DESeq.

THRESHOLD <- 0.05 A.cds.sig <- subset(A.cds.result, pval<THRESHOLD) ## A.cds.result was generated from DESeq B.cds.sig <- subset(B.cds.result, pval<THRESHOLD) ## B.cds.result was generated from DESeq library(VennDiagram) pdf("venn_diagram.pdf") venn.plot <- venn.diagram(list(A.cds.sig$id, B.cds.sig$id), NULL, fill=c("red", "green"), alpha=c(0.5,0.5), cex = 2, cat.fontface=4, category.names=c("Condition A", "Condition B")) grid.draw(venn.plot) dev.off()

Here I used grid::grid.draw function to generate the PDF, because the venn.diagram complains generating PDF. I have manually changed the position and font size of the category legends in the figure above. However, there are some parameters you can adjust in the venn.diagram function to set the legends, layout, transparency (alpha-channel), etc.