Cytoscape COLOUR EDGES

Question

[SKY]

I have a final network which i have made by merging 4 sets of inteactions and now want to colour the edges of the 1st set of interactions with a certain colour.

I need help. I am not able to accomplish this.

Thanks, SKY

[Scooter]

Can you provide a little more information? Exactly what are you having problems with?

-- scooter

[SKY]

Scooter, Thanks again.

I need to colour the edges of a subset of interaction from a larget set (my larger network). I have the subset interaction file (target V/S node) but do not know to tell cytoscape to understand these interactions and colour them in say "red" in the larger network.

I you need any more information. Let me know.

I am operating on lncRNA target gene networks for rice plants.

Rgrds, SKY

Answer 1

[Scooter]

OK, here is how to proceed. First, add a new column to your "subset interaction file" -- call it "subset" or whatever and just add a 1 or something in that column. For clarity, you may want to call the column "Interaction type" and actually add the subset type in the column. You'll also need to add a new column for the edge name [it probably looks something like: source-node (pp) target-node]. Then you can import that as an edge table, which will add that column. It's probably easier to do all of this as part of your initial import (that is, add the columns to your initial 4 interactions). In any case, once you have that column, it's now an easy matter to set up a discrete mapping based on that column to color your edges.

Hope this helps!