Question: How To Show Gene-Gene Interactions On Linear Scale
1
gravatar for ancient_learner
5.9 years ago by
India
ancient_learner610 wrote:

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

gene interaction visualization • 2.1k views
ADD COMMENTlink modified 5.9 years ago by Ben2.0k • written 5.9 years ago by ancient_learner610
1

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.

ADD REPLYlink written 5.9 years ago by Giovanni M Dall'Olio26k
3
gravatar for Ben
5.9 years ago by
Ben2.0k
Edinburgh, UK
Ben2.0k wrote:

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

ADD COMMENTlink written 5.9 years ago by Ben2.0k

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

ADD REPLYlink written 5.9 years ago by ancient_learner610

No problem, yeah it's a great package

ADD REPLYlink written 5.9 years ago by Ben2.0k

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

ADD REPLYlink written 5.9 years ago by ancient_learner610

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.

ADD REPLYlink modified 5.9 years ago • written 5.9 years ago by Ben2.0k

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

ADD REPLYlink written 5.9 years ago by ancient_learner610
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