Visualizing overlap between gene sets in R using circos plots

Question

[Ridha]

Hey there! Hope you are doing well :)

I have a question regarding making circos plots in R. I have 7 gene sets and would like to visualize the overlap and differences between these gene sets. That can easily be done in metascape website by just uploading your list of gene sets(see below results of uploading my gene sets). However, I would like to use R given its flexiblity. I found multiple packages to make circos plot in R (e.g. chordiagram,circlize), but could not get my head around them because most tutorials I found were directed to other visualizations purposes. My data is a matrix with rows representing genes and columns representing names of gene sets. Values are either 1 or 0 indicating whether this gene is selected or not. As such:

    Set1    Set2    Set3    Set4    Set5    Set6    Set7
Gene1   0   1   0   1   0   1   1
Gene2   1   1   1   1   0   1   1
Gene3   1   0   0   0   1   0   1
Gene4   0   1   1   1   0   1   1
Gene5   1   0   1   0   0   0   0
Gene6   0   1   1   1   0   0   1

Any thoughts on how such a plot can be made in R?. If you have other suggestions to visualize such type of data , that would also be great!

Thanks in advance!

Answer 1

[Alex Reynolds]

Instead of a Circos chord plot, consider exploring using an Eulergrid (UpsetR) plot. Set overlaps (such as those in your dataset) are more appropriate for the Eulergrid-style plot.

[behdad.afzali]

Did you figure this out, Alex? We're having the same issue, but want to plot pathways instead of genes. Any thoughts?