[BioC] RCytoscape not recognizing initiated edge attributes.

[Burak Kutlu]

Just realized that actually the edge attributes are in fact preserved.

> eda(cwB at graph,"mechanism")
              13555|108961                13555|13557 
                 "Binding"                  "Binding" 
              13555|242705                13555|50496 
             "Acetylation" "Transcription regulation" 
               13555|13555                13555|52679 
"Transcription regulation" "Transcription regulation" 
...
...


On Mar 15, 2012, at 10:46 PM, Burak Kutlu wrote:

> Hello
> I have issues in getting RCytoscape to recognize edge attributes.
> What I am doing wrong?
> Thanks!
> -burak
> 
> rlNt();runNt("send2RCy")
> entering RCytoscape::displayGraph
> sending 11 nodes
> sending 22 edges
> adding node attributes...
> [1] "label"
> [1] "moleculeType"
> adding edge attributes...
> [1] "weight"
> Error!  RCytoscape::setEdgeAttributes, attributes not initialized. You must call
>        initEdgeAttribute (graph, attribute.name, attribute.type, default.value)
>        where attribute type is one of "char", "integer", or "numeric".
>        example:  g <- initEdgeAttribute (g, "edgeType", "char", "protein-protein interaction")
> [1] "mechanism"
> Error!  RCytoscape::setEdgeAttributes, attributes not initialized. You must call
>        initEdgeAttribute (graph, attribute.name, attribute.type, default.value)
>        where attribute type is one of "char", "integer", or "numeric".
>        example:  g <- initEdgeAttribute (g, "edgeType", "char", "protein-protein interaction")
> [1] "effect"
> Error!  RCytoscape::setEdgeAttributes, attributes not initialized. You must call
>        initEdgeAttribute (graph, attribute.name, attribute.type, default.value)
>        where attribute type is one of "char", "integer", or "numeric".
>        example:  g <- initEdgeAttribute (g, "edgeType", "char", "protein-protein interaction")
>> 
>> cwB at graph
> A graphNEL graph with directed edges
> Number of Nodes = 11 
> Number of Edges = 22 
> 
> eda(cwB at graph)
> Error in match(x, table, nomatch = 0L) : 
>  argument "edge.attribute.name" is missing, with no default
> 
> #######
> # my original graph object
> 
>> edgeData(e2fSubGr)
> $`13555|108961`
> $`13555|108961`$weight
> [1] 1
> 
> $`13555|108961`$mechanism
> [1] "Binding"
> 
> $`13555|108961`$effect
> [1] "Inhibition"
> 
> ...
> ...
> 
> 
>> sessionInfo()
> R version 2.14.2 (2012-02-29)
> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
> 
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base     
> 
> other attached packages:
> [1] RCytoscape_1.5.2      XMLRPC_0.2-4          org.Mm.eg.db_2.6.4   
> [4] RSQLite_0.11.1        DBI_0.2-5             AnnotationDbi_1.16.19
> [7] Biobase_2.14.0        graph_1.32.0          BiocInstaller_1.2.1  
> 
> loaded via a namespace (and not attached):
> [1] IRanges_1.12.6 RCurl_1.91-1   tools_2.14.2   XML_3.9-4