5

Gephi has a great functionality to size nodes based on a given variable. The nodes seem to be sized so that the radius of the circle is linearly proportional to the value of the variable. How do I get the area of the circle to be proportional to the value of the variable?

Using the spline functionality to get exact proportionality seems quite complicated. I imagine one solution might be to export the node table, calculate the square root of the variable, and re-import the data. I was wondering whether I am missing any more direct solution.

Example of radius proportional symbols, using data from Martin Grandjean's tutorial

Yannis P.
  • 2,745
  • 1
  • 24
  • 39
Stefano
  • 51
  • 2
  • Interesting question. Out of curiosity how did you find out that the size of the node is proportional to the radius? My way to go would be to compute a different size by Python or R or even Cytoscape and then save the graph in GraphML and load to Gephi but not directly inside Gephi – Yannis P. Feb 18 '16 at 08:22
  • 1
    Concerning the proportionality: my impression was confirmed by reading various tutorials, and finally simply measuring sizes with a ruler. Sure, I would use Python, R, or D3js, but I am writing down a Gephi tutorial -- so in this particular case, the tool is fixed. Also, I personally think this is a rather important issue. A area/radius proportional option in the software would be great. – Stefano Feb 18 '16 at 08:49
  • you could substitute all your data with square roots. Then the area would be proportional to the value – Vorsprung Feb 18 '16 at 11:25
  • Thanks Vorsprung. Yes, that's what I was suggesting in the second paragraph of my original post, and I would do that. However, that's not quite optimal for non-expert users, who might not be aware of the issue, as it is rather concealed, despite being a clear violation of the principle of graphical integrity. Actually, edit one line of code, so that the square root of any selected value is taken before drawing, would solve the problem at its root -- possibly making Gephi a better (although already great) visualization tool. – Stefano Feb 18 '16 at 11:55

1 Answers1

0

Calculating the square root would be valid if we were displaying squares. But since we are displaying circles, the correct Excel formula would probably be:

=SQRT(*value here*/(2*PI()))
user4157124
  • 2,809
  • 13
  • 27
  • 42