CellNOptR: cutAndPlotResultsTN – R documentation

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cutAndPlotResultsTN

Plot the results of an optimisation at tN

Description

This function takes a model and an optimised bitstring, it cuts the model according to the bitstring and plots the results of the simulation along with the experimental data. This function is designed to work on results of a 2 step optimisation.

Usage

cutAndPlotResultsTN(CNOlist, model, bStrings, plotPDF = FALSE, tag=NULL, 
    plotParams = list(maxrow = 10))

Arguments

`CNOlist`	a CNOlist, corresponding to the optimisation one
`model`	a model (the full one that was used for optimisation)
`bStrings`	a list of bitstring at different time points
`plotPDF`	TRUE or FALSE, tells whether you want a pdf to be produced or not
`tag`	NULL or string; tells whether you want to prefix filenames with a tag (replaces the default behaviour).
`maxrow`	maximum number of row in the plot.
`plotParams`	a list of option related to the PDF and plotting outputs. (1) maxrow is the maximum number of row used to plot the results. See plotOptimResultsPan for other fields.

Value

This function returns plotted MSEs

Note

New in version 1.3.28

Author(s)

T. Cokelaer, A. MacNamara, Sarah Schrier, C. Terfve based on cutAndPlotResultsT1

Examples

#load data

data(CNOlistToy2,package="CellNOptR")
data(ToyModel2,package="CellNOptR")

#pre-process model
model = preprocessing(CNOlistToy2, ToyModel2)

#optimise t1
ToyT1<-gaBinaryT1(
	CNOlist=CNOlistToy2,
	model=model,
	maxGens=20, 
	popSize = 10,
	verbose=FALSE)

#Optimise T2
ToyT2<-gaBinaryTN(
	CNOlist=CNOlistToy2,
	model=model,
	bStrings=list(ToyT1$bString),
	maxGens=20, 
	popSize = 10,
	verbose=FALSE)

cutAndPlotResultsTN(
	CNOlist=CNOlistToy2,
	model=model,
	bStrings=list(ToyT1$bString, bStringT2=ToyT2$bString),
	plotPDF=FALSE)

CellNOptR

Training of boolean logic models of signalling networks using prior knowledge networks and perturbation data

v1.36.0

GPL-3

Authors

T.Cokelaer, F.Eduati, A.MacNamara, S.Schrier, C.Terfve, E.Gjerga, A.Gabor

Initial release

2018-11-08