[BioC] RCytoscape not recognizing initiated edge attributes.
Paul Shannon
pshannon at fhcrc.org
Fri Mar 16 17:25:05 CET 2012
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
>
More information about the Bioconductor
mailing list