pySTDLM.NetworkVisualization Namespace Reference

Functions
	plotReactionNetwork (sim, filename, collapseReversible=False)
	plotCMEReactionNetwork (sim, filename, withRxnNodes=False, collapseReversible=False)
	plotRDMEReactionNetwork (sim, filename, collapseReversible=False)
	plotCMEDynamicReactionNetwork (sim, filename, outfile, stride=1, showMax=False, showMin=False, threshold=-1, replicate=1)

Variables
bool	hasGexf = True

Function Documentation

plotCMEDynamicReactionNetwork()

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)

Args:
    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)

plotCMEReactionNetwork()

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

Plot the reaction scheme as a network 

Args:
    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)

Here is the caller graph for this function:

plotRDMEReactionNetwork()

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

Plot the reaction scheme as a network 

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

Here is the caller graph for this function:

plotReactionNetwork()

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

Plot the reaction scheme as a network 

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

Here is the call graph for this function:

Variable Documentation

hasGexf

bool pySTDLM.NetworkVisualization.hasGexf = True