pySTDLM.NetworkVisualization Namespace Reference

Functions
def	plotReactionNetwork
	Plot the reaction scheme as a network. More...
def	plotCMEReactionNetwork
	Plot the reaction scheme as a network. More...
def	plotRDMEReactionNetwork
	Plot the reaction scheme as a network. More...
def	plotCMEDynamicReactionNetwork
	Plot the dynamics of the species on the network into a dynamic graph file (extension: .gexf) More...

Variables
	hasGexf = True

Function Documentation

def pySTDLM.NetworkVisualization.plotCMEDynamicReactionNetwork	(		sim,
			filename,
			outfile,
			stride = 1,
			showMax = False,
			showMin = False,
			threshold = -1,
			replicate = 1
	)

Plot the dynamics of the species on the network into a dynamic graph file (extension: .gexf)

Parameters

sim	A CMESimulation object
filename	An file from which to read
outfile	A filename for which to output without the extension (.gexf)
stride	Stride through the times (Default=1)
showMax	Show the maximum value achieved over the timecourse on the node (Default=False)
showMin	Show the maximum value achieved over the timecourse on the node (Default=False)
threshold	Only show nodes that attain this value for at least one timepoint of the simulation. Set -1 to show all nodes (Default=-1)
replicate	The replicate to show (Default=1)

def pySTDLM.NetworkVisualization.plotCMEReactionNetwork	(		sim,
			filename,
			withRxnNodes = False,
			collapseReversible = False
	)

Plot the reaction scheme as a network.

Parameters

sim	An CMESimulation object
filename	A file to which to output
withRxnNodes	Plot the graph with reactions as nodes (default: false)
collapseReversible	Collapsee reversible reactions into one node (default: false)

def pySTDLM.NetworkVisualization.plotRDMEReactionNetwork	(		sim,
			filename,
			collapseReversible = False
	)

Plot the reaction scheme as a network.

Parameters

sim	An RDMESimulation object
filename	A file to which to output
collapseReversible	Collapsee reversible reactions into one node

def pySTDLM.NetworkVisualization.plotReactionNetwork	(		sim,
			filename,
			collapseReversible = False
	)

Plot the reaction scheme as a network.

Parameters

sim	An RDMESimulation or CMESimulation object
filename	A file to which to output
collapseReversible	Collapsee reversible reactions into one node

Variable Documentation

pySTDLM.NetworkVisualization.hasGexf = True