toSBGN: Convert a BioPAX OWL file to SBGNML

In cannin/paxtoolsr: Access Pathways from Multiple Databases Through BioPAX and Pathway Commons

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

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

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

cannin/paxtoolsr documentation built on Feb. 2, 2023, 11:44 a.m.