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R: Simulate the model and plot the obtained with the different...

plotLBodeModelSim

R Documentation

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

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

	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

Examples

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

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(CNORode)
Loading required package: CellNOptR
Loading required package: RBGL
Loading required package: graph
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: hash
hash-2.2.6 provided by Decision Patterns

Loading required package: ggplot2
Loading required package: RCurl
Loading required package: bitops
Loading required package: Rgraphviz
Loading required package: grid
Loading required package: XML

Attaching package: 'XML'

The following object is masked from 'package:graph':

    addNode

Loading required package: genalg

Attaching package: 'CNORode'

The following object is masked from 'package:stats':

    simulate

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/CNORode/plotLBodeModelSim.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotLBodeModelSim
> ### Title: Simulate the model and plot the obtained with the different
> ###   experimental conditions.
> ### Aliases: plotLBodeModelSim
> 
> ### ** Examples
> 
>     	library(CNORode)
> 	data("ToyCNOlist",package="CNORode");
> 	data("ToyModel",package="CNORode");
> 	data("ToyIndices",package="CNORode");
> 	modelSimulation=plotLBodeModelSim(cnolistCNORodeExample, model,indices=indices);
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>