[BioC] RCytoscape not recognizing initiated edge attributes.

[Burak Kutlu]

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