How To Show Gene-Gene Interactions On Linear Scale

Question

[ancient_learner]

Hi I want to plot the interactions among the genes within a chromosome. i know circos but i want the linear plot. so can anybody suggest any tool? any R packages willalso be welcomed

[Giovanni M Dall'Olio]

There is an old trick to convert a circos circular image to linear. Open the image in gimp, select RGB mode, and apply Filters->Distort->Polar Coordinates.

Answer 1

[Ben]

arcdiagram, e.g. here's one I made earlier.

[ancient_learner]

seems to be very nice thanks. I was in great need of it

[Ben]

No problem, yeah it's a great package

[ancient_learner]

I want to show the interactions (cis and trans) by grouping them on the basis of chromosomes how to do that?

[Ben]

I'd maybe use different node colours per chromosome and then the cis and trans become obvious ( though I'd plot cis/trans separately if you're looking at several chromosomes). I found the documentation pretty helpful but if you need help you could edit your question with some example data and a description of what you want and I/others will try to create it.

[ancient_learner]

thank you very much ben i tried coloring nodes based on chromosomes and got exactly what i wanted.