writeReport {CellNOptR} | R Documentation |
This function writes a short report of a CellNOptR analysis in an html page, that is linked to the various graphs produced
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)
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 |
resE |
a vector with named entries t1, t2 t1andt2, as produced by the function
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Future versions of this function might directly write and compile a tex file.
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.
C. Terfve
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)