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 >