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tmuetze / Bioconductor_RCy3_the_new_RCytoscape

Update RCytoscape to work for Cytoscape 3.0 and higher using CyREST
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addGraphToGraph #4

Closed pshannon-bioc closed 9 years ago

pshannon-bioc commented 9 years ago

Implementing this method would be a huge help to me.
Right now I see:

selectMethod("addGraphToGraph", "CytoscapeWindowClass") Method Definition: function (obj, other.graph) {}

Perhaps a good start would be to add message("not yet implemented") followed by a real implementation when you can.

For background: this method is really valuable because the Bioc graph class does not support multiple edges between two nodes. In that sense, the graph class (and the graphNEL derived class) are true to the formal definition of a mathematical graph. But practically, this restriction makes it difficult to represent biological networks. The cytoscape network data structure -does- support multiple edges between nodes. Thus "addGraphToGraph" allows us to create multiple true graphs (just one edge between nodes) and then combine them in Cytoscape.

Thanks!

pshannon-bioc commented 9 years ago

Great, Tanja. I’ll give it a go.

On May 17, 2015, at 9:02 AM, Tanja notifications@github.com wrote:

Closed #4.

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