plotLBodeFitness {CNORode} | R Documentation |
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.
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) )
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 |
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. |
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.
Returns a list with simulated data that has the same structure as the cnolist$valueSignals. One matrix for each time-point.
David Henriques, Thomas Cokelaer
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);