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pyLM
v1.1
A Python Problem Solving Environment for the simulation of stochastic biological systems
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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 | |
def pySTDLM.NetworkVisualization.plotCMEDynamicReactionNetwork | ( | sim, | |
filename, | |||
outfile, | |||
stride = 1 , |
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showMax = False , |
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showMin = False , |
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threshold = -1 , |
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replicate = 1 |
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) |
Plot the dynamics of the species on the network into a dynamic graph file (extension: .gexf)
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 , |
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collapseReversible = False |
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) |
Plot the reaction scheme as a network.
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 |
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) |
Plot the reaction scheme as a network.
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 |
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) |
Plot the reaction scheme as a network.
sim | An RDMESimulation or CMESimulation object |
filename | A file to which to output |
collapseReversible | Collapsee reversible reactions into one node |
pySTDLM.NetworkVisualization.hasGexf = True |