Re: how to layout a bipartite network

[Ugur Dogrusoz]

Hi there,

 

the answer depends on what you mean by "display/layout a bipartite network". for instance, you could indicate / highlight the nodes in two bipartitions by simply dedicating a distinct shape or color to each partition. if your goal is to specifically display the bipartite graph in the conventional way of  two columns of nodes (left column containing the nodes in one parititon, right column similarly containing the nodes in the second one), then you could use the crossing minization idea in Sugiyama layout (for only two "layers") [1][2]. This is an iterative algorithm with crossing minimization between two layers being the core sub-algorithm applied again again. Techniques used for this purpose vary considerably, one simple idea is placing the nodes in the second layer at the "barycenter" of its parents (neighbors) in the first layer (and vice versa).

 

cheers,

Ugur 

 

[1] http://en.wikipedia.org/wiki/Layered_graph_drawing

[2] http://improbable-emancipation.blogspot.com/2011/09/sugiyama-layout-algorithm-hierarchical.html

[Simone Gabbriellini]

Hi Ugur,

well, being able to indicate nodes by dedicating a distinct shape and color to each partition would be a first start... I am able to filter one partition but not to change properties using Vizmapper... the only option I find is to change shape and color individually for each of the selected nodes, which is an infeasible task in my network. Any suggestion welcome!

thanks for pointing the layout approach by Sugiyama, I will look into it.

Best,

Simone

2013/5/6 Ugur Dogrusoz <ugurdo...@gmail.com>

--
You received this message because you are subscribed to the Google Groups "cytoscape-discuss" group.
To unsubscribe from this group and stop receiving emails from it, send an email to cytoscape-disc...@googlegroups.com.
To post to this group, send email to cytoscap...@googlegroups.com.
Visit this group at http://groups.google.com/group/cytoscape-discuss?hl=en.
For more options, visit https://groups.google.com/groups/opt_out.
 
 

--
Simone Gabbriellini, PhD

PostDoc@DISI, University of Bologna
mobile: +39 340 39 75 626
email: simone.ga...@unibo.it
academia.edu: http://goo.gl/7pq62

DigitalBrains srl
Amministratore
mobile: +39 340 39 75 626
email: simone.ga...@digitalbrains.it
home: www.digitalbrains.it