toSBGN {paxtoolsr} | R Documentation

## 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)

[Package paxtoolsr version 1.22.0 Index]