Help with edges direction in Cytoscape 3

[Miquel Oltra]

Hi!

Does anyone knows which edge attributes determine the direction of one edge? It is controlled only by one column or is it a combination of some columns?

I think it should be a simple question, but I have found some troubles with that.

I'm using Cytoscape 3.1 and testing with some signaling pathways imported from Reactome in BioPAX3 format.

Any help will be very appreciated!

Best regards,
Miquel Oltra
Ph.D. Student
Valencia

[Scooter Morris]

Hi Miquel,
   The direction of the edge is implicitly defined by the source and target of the edge when it is created.  You can add arrows to either the source or target ends of the edge in the Style section of the Control Panel.

-- scooter

[Miquel Oltra]

Hi Scooter!

Thanks for the reply, I understand. However, when the network is created dynamically importing it from an URL (from Reactome in this case), I guess that the directions are written in Cytoscape depending on the values specified on the chosen format, isn't it?

For instance, I'm generating a network importing the BioPAX3 URL from a Reactome pathway. When I visualize it in Cytoscape, I have some kind of edges which "interaction" values are "contains" (there is no name information, only the type of interaction). If I select one edge and then the "zoom selected region" button, the graph point me at the exact edge.

So, the question is: how does cytoscape knows which "contains" edge on the graph belongs to the exact row "contains" on the table panel? In my example there are more than 50 rows on the edge table of the table panel that looks like the same row (they have only information on the interaction column). 

Is there any file storing that information?

If my explanation is not good or clear enough, please feel free to tell it and I will try to give you more examples.

Thanks in advance,

Miquel

[Scooter Morris]

Hi Miquel,
    Internally, each edge is given a unique identifier (SUID).  When you import from Reactome, Cytoscape generates identifiers for all nodes and edges as they are imported.  The internal representation of an edge is a pair of nodes with all of the "other" information stored in the table (including "contains").  By convention (carried over from Cytoscape 2, where it was mandatory), we name our edges with the source and target nodes, but that's not required. 

-- scooter

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[Miquel Oltra]

Hi Scooter,
thanks a lot, I see!

Do you know if I can see this SUID somewhere on my laptop?

Best regards,
Miquel

[Scooter Morris]

Sure, it's one of the columns in the table. Do a show all in the edge
table (double check) and you should see it.

-- scooter

[Miquel Oltra]

Ahh ok!!

Sorry, I haven't seen this option. Thanks for your time and help.

Regards,

Miquel

El divendres, 3 abril de 2015 23:04:23 UTC+2, Scooter Morris va escriure: