package: VennDiagram

pdf('./venn.pdf')
grid.obj = venn.diagram(list(A=1:53, B=3:23, C=33:70), filename=NULL)
grid.draw(grid.obj)
dev.off()

package: limma

One can use functions in limma pacakge to plot a Venn diagram in R.

biocLite("limma")
library(limma)
hsb2<-read.table("http://www.ats.ucla.edu/stat/R/notes/hsb2.csv", sep=',', header=T)
attach(hsb2)

hw<-(write>=60)
hm<-(math >=60)
hr<-(read >=60)
c3<-cbind(hw, hm, hr)
# c3 is a matrix with logical values.
a <- vennCounts(c3)
vennDiagram(a)

Reference: http://www.ats.ucla.edu/stat/r/faq/venn.htm