Super position of small network over big network

Question

I am working on PPI network and for the network plot I am using Gephi and rgexf package. In my network there are 9453 no. of vertices and 36888 connections. So, when plot the network on gephi we can't analyse anything, so I plot only top 50 nodes network. Now I want to highlight that 50 node's network over the top 100 nodes network. Here the top means the nodes which has highest degree. So is there any way to do it?

This the plot for top 50 nodes, there is one node which is not connected to any of the node in top50:

I am struggling from few days.

Answer 1

UPDATE - I updated the descriptions

Ok so this is not totally trivial but not straightforward either. I have created a random network with 500 nodes to show you an example.

1. After you load your network with Gephi you need at least to run the Average degree from the statistics.
2. You then go to the Filters section, select Attributes>Range>In-degree, double-click and press the Filter button (Note: In your case you should just see Degree but the rest still apply)
3. Move the slider to the right so that in the Context panel the number of remaining nodes reaches ~50

Here is how it looks for me

COLORING:

While you keep the Filter button pressed you can apply a different color to the filtered nodes. In my case I went in Ranking>Nodes selected InDegree and applied a green color. Note that you can also select Degree to get the effect you want. The respective panel looks like that:

This colors only the filtered nodes. Alternatively, you can apply the node brush but then it becomes a bit dull :). There is a 3rd option but I leave it as an exercise :).

The final graph looks like that for me.

Programmatically you could do something similar in igraph. You can select the nodes with top-50 indegrees, assign them a color, assign all the rest a different color and export to GraphML.

I hope it helped.