[BioC] RCytoscape not recognizing initiated edge attributes.

[Paul Shannon]

Hi Burak,

Glad this worked out.

I often use attribute querying methods by first reminding myself what attributes have been defined:

   eda.names (<graph>)   # "mechanism", "edgeType", "weight"

then to extract an attribute of interest, just like you did

   eda (<graph>, "mechanism") 

The node attribute querying methods are just the same:  noa.names (<graph>); noa (<graph>, <attribute.name>)

 - Paul


On Mar 15, 2012, at 11:04 PM, Burak Kutlu wrote:

> 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  
>