plotLBodeModelSim {CNORode} | R Documentation |
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 |
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
library(CNORode) data("ToyCNOlist",package="CNORode"); data("ToyModel",package="CNORode"); data("ToyIndices",package="CNORode"); modelSimulation=plotLBodeModelSim(cnolistCNORodeExample, model,indices=indices);