Incremental hierarchical layout in Cytoscape

[Gloria Kreitinger]

I would like to make a tripartite network in Cytoscape, where I have three different types of nodes with a defined hierarchy.  I have node types A, B, and C, A-B edges and B-C edges.  I would first like to create a hierarchical graph using only A and B nodes and then, keeping the A/B network structure the same, incrementally add the second set of B-C edges on top.

Figure 5.36 from this site describes exactly what I want to do: http://docs.yworks.com/yfiles/doc/developers-guide/incremental_hierarchical_layouter.html

 

However, I cannot find an easy way to do this in Cytoscape.

Is this possible in Cytoscpae 3.1?

Much thanks,

Gloria

[piet molenaar]

Hi Gloria,

This should be possible by using the hierarchical layout on selected nodes only (A and B, you'd have to annotate these with an attribute in a data column to select these). Subsequent scaling enables hierarchical laout of subsections; something along the lines depicted below...

Hope this helps,

Piet

Select

Apply: Layout>Hierarchical>Selected Nodes

Scale rotate and move

Apply bundling

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Piet Molenaar
piet...@gmail.com
Department of Oncogenomics, M1-131
Academic Medical Center
University of Amsterdam
Meibergdreef 9
1105 AZ Amsterdam
the Netherlands

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