Simulate the model and plot the obtained with the different experimental conditions.

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Description

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.

Usage

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	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=T)

Arguments

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

show the error (defaults to TRUE)

Value

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

Author(s)

David Henriques, Thomas Cokelaer

See Also

CellNOptR createLBodeContPars

Examples

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

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