[BioC] RCytoscape not recognizing initiated edge attributes.
Burak Kutlu
bkutlu at systemsbiology.org
Fri Mar 16 07:04:28 CET 2012
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
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