paxtoolsr (version 1.6.3)

toSBGN: Convert a BioPAX OWL file to SBGNML

Description

This function will convert a BioPAX OWL file into the Systems Biology Graphical Notation (SBGN) Markup Language (SBGNML) XML representation

Usage

toSBGN(inputFile, outputFile = NULL)

Arguments

inputFile

a string of the name of the input BioPAX OWL file

outputFile

a string of the name of the output SBGNML file

Value

• see readSbgn()

concept

paxtoolsr

Details

Objects in the SBGNML format are laid out using a Compound Spring Embedder (CoSE) layout

References

http://www.cs.bilkent.edu.tr/~ivis/layout/cose-animated-demo/cose.html

Examples

outFile <- tempfile()
results <- toSBGN(system.file("extdata", "biopax3-short-metabolic-pathway.owl", 
  package="paxtoolsr"), 
  outFile)