Re: [Cytoscape-discuss] RCytoscape and Adjacency Matrix

[Paul Shannon]

Hi Dave,

The vignette explains all of these things -- and if things are left out, I will be glad to add them.

Try this to see the vignette:

> library (RCytoscape)
> browseVignettes ('RCytoscape')

Further detail -- a full-featured sample graph, and how to display it -- can be viewed this way:


> RCytoscape::makeSimpleGraph
> RCytoscape::demoSimpleGraph

Let me know if you get stuck.

- Paul

On Jul 20, 2012, at 8:44 PM, Dave wrote:

> I am creating a graph using RCytoscape based off of a Adjacency matrix.
>
> I have followed this example:
>
> http://rcytoscape.systemsbiology.net/versions/current/cookbook/randomAM/index.html
>
> I have specficied the graph as being directed, yet there are no directional arrows when the graph is opened in cytoscape. Also, I am initializing and setting my edges as numerical float values and I do not see them being sent across to Cytoscape.
>
> Is this example correct? In order to achieve the above (make my edges directional) and transmit edge attributes. What do I have to do in addition to what has been done in the posted example.
>
> Thanks,
>
> Dave
>
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