plotLBodeModelSim: Simulate the model and plot the obtained with the different...
In CNORode: ODE add-on to CellNOptR

Description Usage Arguments Value Author(s) See Also Examples

Plots the simulated values of the logic based ODE model. Only dynamic states are plotted, i.e. those that are not inputs. a blue line. Additionally this functions returns the the simulated values.

	plotLBodeModelSim(cnolist, model, ode_parameters = NULL, indices = NULL, 
	adjMatrix = NULL, timeSignals=NULL, time = 1, verbose = 0, transfer_function = 3,
	reltol = 1e-04, atol = 0.001, maxStepSize = Inf, maxNumSteps = 1e+05,
	maxErrTestsFails = 50, large = FALSE, nsplit = 4, show = TRUE)

`cnolist`	A list containing the experimental design and data.
`model`	The logic model to be simulated.
`ode_parameters`	A list with the ODEs parameter information. Obtained with `createLBodeContPars`.
`indices`	Indices to map data in the model. Obtained with indexFinder function from CellNOptR.
`adjMatrix`	Model representation in the form of an adjacency matrix. When not provided will be automatically computed based in the model.
`timeSignals`	An array containing a different timeSignals. If you use this argument, it will also modify the dimensions from valueSignals.
`time`	An integer with the index of the time point to start the simulation. Default is 1.
`verbose`	A logical value that triggers a set of comments.
`transfer_function`	The type of used transfer. Use 1 for no transfer function, 2 for Hill function and 3 for normalized Hill function.
`reltol`	Relative Tolerance for numerical integration.
`atol`	Absolute tolerance for numerical integration.
`maxStepSize`	The maximum step size allowed to ODE solver.
`maxNumSteps`	The maximum number of internal steps between two points being sampled before the solver fails.
`maxErrTestsFails`	Specifies the maximum number of error test failures permitted in attempting one step.
`large`	Boolean variable defining if the plot should split into several subplots.
`nsplit`	In case the large plot options is selected define how many subplots will exist. Default is 4.
`show`	Boolean variable defining if we shold plot the CNOlist object.

Returns a list with simulated Model values. One matrix of size number of species by number of experimental conditions for each time-point.

David Henriques, Thomas Cokelaer

CellNOptR createLBodeContPars

    	library(CNORode)
	data("ToyCNOlist",package="CNORode");
	data("ToyModel",package="CNORode");
	data("ToyIndices",package="CNORode");
	modelSimulation=plotLBodeModelSim(cnolistCNORodeExample, model,indices=indices);