toSBGN: Convert a BioPAX OWL file to SBGNML

Description Usage Arguments Details Value References Examples

View source: R/toSBGN.R

Description

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

Usage

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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

Details

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

Value

see readSbgn()

References

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

Examples

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

cannin/paxtoolsr documentation built on Oct. 5, 2018, 11:23 p.m.