export_cytoscape {ontoFAST}

Export to Cytoscape format

Description

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!

Usage

export_cytoscape(
  ontology,
  annotations = "auto",
  is_a = c("is_a"),
  part_of = c("BFO:0000050")
)

Arguments

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

Value

Returns a table

Examples

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")