venn diagram for gene lists using R

Question

[chrisclarkson100]

I have 3 lists of genes from gene cards, GO and NCBI Gene. I'm trying to see how much they overlap- using an interactive program where I can take their intersection lists- using venn diagrams and remove and add genes.

Is this possible using R programming?

Answer 1

[Renesh]

Use Vennerable package in R. It can display venn diagram for upto 9 sets. It can also produce weighted venn diagrams. To install it,

install.packages("Vennerable", repos="http://R-Forge.R-project.org";)

Here is command for 3 sets

vennD=Venn(SetNames = c("Samp1", "Samp2","Samp3"), Weight=c(`100`=x,`010`=x,`110`=x,`001`=x,`101`=x,`011`=x,`111`=x))

x is the any number corresponding to set (e.g. 111 means common to all samples)

plot(vennD, doWeights = FALSE, type = "circles")

Development page: https://r-forge.r-project.org/R/?group_id=474

Answer 2

[Jorjial]

You can use the R package VennDiagram to plot the Venn diagrams and use shiny from RStudio to visualise the results in a web browser dynamically. In the web page created with Shiny, you can show the lists and let the users to create their own plots.