Description Usage Arguments Value Examples
View source: R/Viz_manipul_main.R
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!
1 2 3 4 5 6 | 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
1 2 3 4 5 6 7 8 9 10 11 12 | 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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