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
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.
arcdiagram, e.g. here's one I made earlier.
seems to be very nice thanks. I was in great need of it
No problem, yeah it's a great package
I want to show the interactions (cis and trans) by grouping them on the basis of chromosomes how to do that?
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.
thank you very much ben i tried coloring nodes based on chromosomes and got exactly what i wanted.