
Hi there,
I am trying to build a protein expression network. I am currently using a n^2 symmetrical matrix, my main problem is that I cannot work out how to set the distances between nodes based upon the corresponding values in the matrix. For instance a simplified
version:
A B C
A 1 3 1
B 3 1 2
C 1 2 1
What I would want is A and C to be clustered together closer than A & B if that makes sense.
Is this sort of thing possible in nodeXL?
Thanks,
Gareth



Gareth:
If you use the FruchtermanReingold layout (NodeXL, Graph, Layout), and you add an Edge Weight column to the Edges worksheet (the column name has to be spelled
exactly like that), then edges with a larger edge weight will exert a stronger "force" on each other and will tend to end up closer to each other when you refresh the graph. (FruchtermanReingold is what's called a "forcedirected" layout algorithm.)
The effect varies quite a bit with the number of vertices, number of edges, and the way they are connected, but it might be worth a try in your case.
If your matrix is in a plain Excel workbook and you use NodeXL, Data, Import From Open Matrix Workbook to get your data into NodeXL, then NodeXL will add the Edge Weight column for you.
 Tony

