Betweenness centrality or betweenness unDir which one should I use to plot centralities on an undirected network?

Question

[carolinapr.rocha]

Hi everyone. I´m on cytoscape with an undirected network and I want to plot centralities (degree/betweenness), but the values of Betweenness centrality and betweenness unDir are really divergent, and I don´t know which value should I use.

[Lars Juhl Jensen]

When I use NetworkAnalyzer on an undirected network in Cytoscape, I get only a single between centrality metric per node. Where does the one you call "unDir" come from? I cannot find it.

[carolinapr.rocha]

It is not directly on Network statistics to see the unDir, in Table Panel, I go to show columns and select Betweenness unDir, Betweenness centrality and Degree.

[Lars Juhl Jensen]

That is also where I am looking, but I only get Betweeness centrality (and Degree etc.) but not Betweenness unDir. Are we using the same version of Cytoscape and NetworkAnalyzer? I am on Cytoscape 3.4.0 and latest NetworkAnalyzer.

[carolinapr.rocha]

Im using cytoscape 3.4.0

[carolinapr.rocha]

Im also using Centiscape

[Lars Juhl Jensen]

I did a little bit of Googling. Are you by any chance using CentiScaPe instead of the built-in NetworkAnalyzer?

Answer 1

[Lars Juhl Jensen]

When calculating betweenness centrality and several other network metrics, it matters if the network is directed or not directed. Betweenness centrality of nodes can be calculated in Cytoscape in at least two different ways: by using the built-in NetworkAnalyzer (in the tools menu) or by using the CentiScaPe app. The reason why this matters is that betweenness comes down to counting how many (or which fraction of) paths go through a given node. For a directed network, the paths must follow the correct directions of the edges. For an undirected network, all edges are considered bidirectional and paths can thus go either way through an edge.

NetworkAnalyzer will prompt the user whether the network should be considered directed or not directed and calculate metrics accordingly, putting the betweenness centrality of each node in a column called BetweennessCentrality. In CentiScaPe the user also has to select, but the resulting columns have different names (Betweenness Dir and Betweeness unDir for directed and undirected networks, respectively).

If your network is undirected, you should always use the undirected version of the metrics. The directed version will be meaningless since it involves assigning arbitrary directions to undirected edges. In case you wonder, the edges will always be considered as pointing from the column you specified as Source to the one you specified as Target when importing the network.

[carolinapr.rocha]

Thank you so much for clearing that up.