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
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?
If you use the Fruchterman-Reingold 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. (Fruchterman-Reingold is what's called a "force-directed" 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.