plotLBodeFitness: Plot data against simulated values.

Description

Plots the simulated values with the logic-based ODE against the the data contained contained the data contained in the cnolist. The data values are represented with a black line and the simulated values with a blue line. Additionally this functions returns the the simulated values.

Usage

plotLBodeFitness(cnolist, model, ode_parameters = NULL, indices = NULL, 		adjMatrix = NULL, time = 1, verbose = 0, transfer_function = 3, reltol = 1e-04,
		atol = 0.001, maxStepSize = Inf, maxNumSteps = 1e+05, maxErrTestsFails = 50, 		plot_index_signals = NULL, plot_index_experiments = NULL,
plot_index_cues = NULL, colormap="heat", plotParams=list(margin=0.1, width=15, height=12, cmap_scale=1, cex=1.6, ymin=NULL), initial_state=0.1 )

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.

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.

plot_index_signals

In case you only want to plot some signals, provide an integer vector with the indexes.

plot_index_experiments

In case you only want to plot some experiments, provide an integer vector with the indexes.

plot_index_cues

In case you only want to plot some cues, provide an integer vector with the indexes.

colormap

Uses the same colormap as in CellNOptR by default. If set to "green", it uses the deprecated colormap.

plotParams

additional parameters to refine the ploggin. See plotOptimResultsPan function in CellNOptR for more details.

initial_state

initial state of the dynamic nodes (non-measured) (Defaults to 0.1)

Value

Returns a list with simulated data that has the same structure as the cnolist$valueSignals. One matrix for each time-point.

Details

Check CellNOptR for details about the cnolist and the model format. For more details in the configuration of the ODE solver check the CVODES manual.

Examples

Run this code

	library(CNORode)
	data("ToyCNOlist",package="CNORode");
	data("ToyModel",package="CNORode");
	data("ToyIndices",package="CNORode");
	ode_parameters=createLBodeContPars(model,random=TRUE);
	dataSimulation=plotLBodeFitness(cnolistCNORodeExample, model,indices=indices);