graph::join discards node and edge attributes
0
0
Entering edit mode
Paul Shannon ★ 1.1k
@paul-shannon-578
Last seen 9.6 years ago
I have two well-annotated kegg pathway graphs I wish to merge. Using graph::join, the nodes and edges merge nicely, but all the edge and node attributes are lost, and a new edge attribute 'weight' is added. > names (nodeDataDefaults (g.05200)) [1] "type" "label" "desc" "BP" "MF" "CC" "phase" "score" "lfc" "pval" > names (nodeDataDefaults (g.04010)) [1] "type" "label" "desc" "BP" "MF" "CC" "phase" "score" "lfc" "pval" > names (nodeDataDefaults (g.both)) NULL > names (edgeDataDefaults (g.04010)) [1] "edgeType" "pmid" "abstract" "reciprocal" "score" "source" > names (edgeDataDefaults (g.05200)) [1] "edgeType" "pmid" "abstract" "reciprocal" "score" "source" > names (edgeDataDefaults (g.both)) [1] "weight" Is there any graph method, current or planned, which will preserve node and edge attributes? I realize that attribute conflicts can arise, and some strategy is required to handle these. - Paul > sessionInfo () R version 2.12.0 (2010-10-15) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] en_US.utf-8/en_US.utf-8/C/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_1.1.6 org.Mm.eg.db_2.4.1 RCurl_1.4-3 bitops_1.0-4.1 GOstats_2.16.0 Category_2.16.0 GO.db_2.4.5 [8] GSEABase_1.11.2 annotate_1.28.0 KEGG.db_2.4.1 KEGGgraph_1.4.0 graph_1.26.0 XML_3.2-0 SPIA_1.8.0 [15] org.Hs.eg.db_2.4.6 RSQLite_0.9-2 DBI_0.2-5 AnnotationDbi_1.11.8 Biobase_2.10.0 RUnit_0.4.26 loaded via a namespace (and not attached): [1] genefilter_1.32.0 RBGL_1.25.0 splines_2.12.0 survival_2.35-8 tools_2.12.0 XMLRPC_0.2-2 xtable_1.5-6
graph graph • 703 views
ADD COMMENT

Login before adding your answer.

Traffic: 857 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6