writeReport {CellNOptR} | R Documentation

## Write a report of a CellNOptR analysis

### Description

This function writes a short report of a CellNOptR analysis in an html page, that is linked to the various graphs produced

### Usage

    writeReport(modelOriginal, modelOpt, optimResT1, optimResT2, CNOlist, directory,
        namesFiles = list(dataPlot = NA, evolFitT1=NA, evolFitT2=NA, simResultsT1=NA,
        simResultsT2=NA, scaffold=NA, scaffoldDot=NA, tscaffold=NA, wscaffold=NA,
        PKN=NA, PKNdot=NA, wPKN=NA,nPKN=NA), namesData = list(CNOlist=NA, model=NA),
        resE=NULL)

### Arguments

`modelOriginal` | the original previous knowledge network (i.e. model that you loaded) in a model list format
`modelOpt` | the model that was actually used for optimisation (i.e. the scaffold network, after compression and expansion) in a model list format
`optimResT1` | the results of the optimisation at t1, as output by gabinaryT1
`optimResT2` | the results of the optimisation at t2, as output by gabinaryT2. Set this to NA if you have performed a one time point optimisation.
`CNOlist` | a CNOlist
`directory` | the name of a new directory that will be created, where your results will be moved
`namesFiles` | a list of the names of the files that should have been created. Depending on whether a t2 optimisation was performed or not, all or some of the following fields are expected: dataPlot, evolFitT1, evolFitT2, simResultsT1, simResultsT2, scaffoldDot, scaffold, tscaffold, wscaffold, PKN, PKNdot, wPKN, nPKN.
`namesData` | a list with fields `$CNOlist` and `$model` that contain strings that are meaningful identifiers of your data and previous knowledge network (for your own record).
`resE` | a vector with named entries t1, t2 t1andt2, as produced by the function `ResidualError`, that contains the residual error associated with the discretisation of the data. Since version 1.3.29, there is no need to provide this argument. Kept for back compatibility.

### Details

Future versions of this function might directly write and compile a tex file.

### Value

This function produces a directory and moves all the files of namesFiles to it, then it creates an html report that contains infos about the optimisation process.

### Author(s)

C. Terfve

### See Also

writeNetwork, writeScaffold

### Examples

    tmpdir<-tempdir()
    setwd(tmpdir)

    #load data

    data(CNOlistToy,package="CellNOptR")
    data(ToyModel,package="CellNOptR")

    #pre-process model (partial)

    indicesToy<-indexFinder(CNOlistToy,ToyModel,verbose=TRUE)
    ToyNCNOcutComp<-compressModel(ToyModel,indicesToy)
    indicesToyNCNOcutComp<-indexFinder(CNOlistToy,ToyNCNOcutComp)
    ToyNCNOcutCompExp<-expandGates(ToyNCNOcutComp)

    #optimise

    ToyFields4Sim<-prep4sim(ToyNCNOcutCompExp)
    initBstring<-rep(1,length(ToyNCNOcutCompExp$reacID))
    ToyT1opt<-gaBinaryT1(
    	CNOlist=CNOlistToy,
    	model=ToyNCNOcutCompExp,
    	initBstring=initBstring,
    	maxGens=2,
    	popSize=5,
    	verbose=TRUE)

    #write report

    namesFilesToy<-list(
    	dataPlot=NA,
    	evolFitT1=NA,
    	evolFitT2=NA,
    	simResultsT1=NA,
    	simResultsT2=NA,
    	scaffold=NA,
    	scaffoldDot=NA,
    	tscaffold=NA,
    	wscaffold=NA,
    	PKN=NA,
    	PKNdot=NA,
    	wPKN=NA,
    	nPKN=NA)

    writeReport(
    	modelOriginal=ToyModel,
    	modelOpt=ToyNCNOcutCompExp,
    	optimResT1=ToyT1opt,
    	optimResT2=NA,
    	CNOlist=CNOlistToy,
    	directory="testToy",
    	namesFiles=namesFilesToy,
    	namesData=list(CNOlist="Toy",model="ToyModel"),
    	resE=NA)

[Package CellNOptR version 1.30.0 Index]