venn diagram for gene lists using R
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Entering edit mode
7.7 years ago

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?

R • 19k views
5
Entering edit mode
7.7 years ago
Renesh ★ 2.1k

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

3
Entering edit mode
7.7 years ago
Jorjial ▴ 290

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.