How to pass edge property data from file to cytoscape

[shiva]

Hi,

I'm new to cytoscape. I need to create a network with formatted edges.
e.g.
I have a file containing 3 elements A,B,C
A XX B
B YY C

Here XX and YY are interaction, when i import this file to cytoscape
it creates a basic network.

Now i want a diamond arrow between A - B and a T shape arrow between B
- C.
Can any one please tell me what i need to add in the input file to
achieve the above?

Many Thanks,

[R. Hannes Niedner]

Take a look at the trusty Cytoscape users guide at http://cytoscape.wodaklab.org/wiki/Cytoscape_User_Manual/Network_Formats. I believe a simple SIF file will not be able to accommodate graphical attributes, but if you look under GML and XGMML you may find what you need.

GML Format

In contrast to SIF, GML is a rich graph format language supported by many other network visualization packages. The GML file format specification is available at:

http://www.infosun.fmi.uni-passau.de/Graphlet/GML/

It is generally not necessary to modify the content of a GML file directly. Once a network is built in SIF format and then laid out, the layout is preserved by saving to and loading from GML. Visual attributes specified in a GML file will result in a new visual style named Filename.style when that GML file is loaded.

XGMML Format

XGMML is the XML evolution of GML and is based on the GML definition. In addition to network data, XGMML contains node/edge/network attributes. The XGMML file format specification is available at:

http://www.cs.rpi.edu/~puninj/XGMML/

XGMML is now preferred to GML because it offers the flexibility associated with all XML document types. If you're unsure about which to use, choose XGMML.

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