Import edge direction from networkfile

[mariumw...@gmail.com]

Hello everyone,

I have a network file created using a tool developed by me, the network file looks like this

GeneA     GeneB     <-

GeneB     GeneC     ->

GeneD     GeneC     ->

GeneD     GeneF     <-

Importing the network itself was successfully done, but I am looking for a way to import the directions in the network. Since the directions are not always the same, can somebody tell me how to import such directions into cytoscape. I have looked alot and could not fins the solution.

Best

Mary

[Alex Pico]

Well, there are two approaches:

1. Directional network model. If you want the actual underlying network model to be correct in terms of direction, then you need to pre-define “source” and “target” columns. You can’t import a mix of and expect Cytoscape to know which is source based on an arbitrary symbol in a third column.

2. Directional network appearance. If you don’t care what the actual model is and only need the visualization or appearance of the network be directed, then you can take the same file you’ve already imported and use the column of direction symbols to map discretely to source and target arrowhead types. See manual http://manual.cytoscape.org/en/stable/Styles.html#introduction-to-style

The second approach can produce networks with arrows pointing in the direction you want, but know that network functions that rely on directness (like in-degree/out-degree calculations) use the model, not the visual style and will be wrong if you take this approach.

 - Alex

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