toPajek: Export a network to the Pajek file format

In BoolNet: Construction, Simulation and Analysis of Boolean Networks

Export a network to the Pajek file format

Description

Exports a network to the Pajek file format to visualize transition trajectories. For more information on Pajek, please refer to http://mrvar.fdv.uni-lj.si/pajek/

Usage

toPajek(stateGraph, file = "boolean.net", includeLabels=FALSE, ...)

Arguments

stateGraph	An object of class AttractorInfo or SymbolicSimulation, as returned by getAttractors and simulateSymbolicModel respectively. As the transition table information in this structure is required, getAttractors must be called in synchronous mode and with returnTable set to TRUE. Similarly, simulateSymbolicModel must be called with returnGraph=TRUE. Alternatively, stateGraph can be an object of class TransitionTable, which can be extracted using the functions getTransitionTable, getBasinOfAttraction, or getStateSummary .
file	The name of the output file for Pajek. Defaults to "boolean.net".
includeLabels	If set to true, the vertices of the graph in the output file are labeled with the binary encodings of the states. Defaults to FALSE.
...	This is only for compatibility with previous versions and should not be used.

Value

This function has no return value.

See Also

getAttractors, simulateSymbolicModel, getTransitionTable, getBasinOfAttraction, getStateSummary, toSBML

Examples

## Not run: 
# load example data
data(cellcycle)

# get attractors
attractors <- getAttractors(cellcycle)

# export to Pajek
toPajek(attractors, file="pajek_export.net")

## End(Not run)

BoolNet documentation built on Oct. 2, 2023, 5:08 p.m.