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layoutcytoscape

How to lay out the connection according to different edge colors in cytoscape?

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Here is a connection plot I created in CytoScape. The edge color was set according to a categorical variable. I just want to know how can I lay out the connection according to different edge colors (I want the green edge to be mainly on the right side and the gray left for example). I want to lay out the connection automatically rather than manually.

Any help is appreciated.

Solution

  • The Boundary Layout app may be helpful for this: http://apps.cytoscape.org/apps/boundarylayout

    I think the path would be to use Cytoscape's filter functionality to group nodes that are only connected via grey edges in one group, and nodes that are only connected via green edges in another group, and arrange the layout boundaries where you want them.

    http://manual.cytoscape.org/en/stable/Finding_and_Filtering_Nodes_and_Edges.html#filters