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R: Plot data against simulated values.

plotLBodeFitness

R Documentation

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)

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.

Value

Returns a list with simulated data that has the same structure as the cnolist$valueSignals. One matrix 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");
	ode_parameters=createLBodeContPars(model,random=TRUE);
	dataSimulation=plotLBodeFitness(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/plotLBodeFitness.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotLBodeFitness
> ### Title: Plot data against simulated values.
> ### Aliases: plotLBodeFitness
> 
> ### ** Examples
> 
> 	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);
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>