View source: R/Viz_manipul_main.R
export_cytoscape | R Documentation |
This function converts character annotations to Cytoscape format. It returns a table that can be saved as in csv format and imported in Cytoscape. In Cytoscape choose File -> Import -> Network -> File. Then assign columns to nodes and edges. Do not select columns that enumerate the tables' rows!
export_cytoscape( ontology, annotations = "auto", is_a = c("is_a"), part_of = c("BFO:0000050") )
ontology |
Ontology |
annotations |
which annotations to use: "auto" means automatic annotations, "manual" means manual ones. Alternatively, any other list containing annotations can be specified. |
is_a |
is_a |
part_of |
part_of |
Returns a table
data(HAO) data(Sharkey_2011) data(Sharkey_2011_annot) ontology<-HAO # processing ontology to incorporate character statements ontology<-onto_process(ontology, Sharkey_2011[,1], do.annot = F) # embedding manual annotations ontology$annot_characters<-Sharkey_2011_annot # exporting cyto<-export_cytoscape(ontology, annotations = ontology$annot_characters, is_a = c("is_a"), part_of = c("BFO:0000050")) #write.csv(cyto, file="cyto.csv")
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