Question: venn diagram for gene lists using R
3
gravatar for chrisclarkson100
6.2 years ago by
European Union
chrisclarkson10090 wrote:

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 • 16k views
ADD COMMENTlink modified 6.2 years ago by Renesh1.9k • written 6.2 years ago by chrisclarkson10090
5
gravatar for Renesh
6.2 years ago by
Renesh1.9k
United States
Renesh1.9k wrote:

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 (eg. 111 means common to all samples)

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

 

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

 
ADD COMMENTlink written 6.2 years ago by Renesh1.9k
3
gravatar for Jorjial
6.2 years ago by
Jorjial280
Valencia, Spain
Jorjial280 wrote:

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.

ADD COMMENTlink written 6.2 years ago by Jorjial280
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