plotOptimResultsPDF: Plot the data and simulated values in a pdf file

In cokelaer/CellNOptR: Training of boolean logic models of signalling networks using prior knowledge networks and perturbation data

Description

This is a wrapper for plotOptimResults

Usage

plotOptimResultsPDF(simResults, expResults, times, namesCues, namesSignals,
valueCues, filename, formalism="new")

Arguments

simResults	a list with a field for each time point, each containing a matrix of dimensions number of conditions * number of signals, with the first field being t0. Typically produced by simulating a model and then extracting the columns that correspond to signals
expResults	same as above, but contains the experimental results, ie this is CNOlist$valueSignals
times	a vector of times, its length should be the same as the number of fields in simResults and ExpResults
namesCues	a vector of names, typically CNOlist$namesCues
namesSignals	a vector of names, typically CNOlist$namesSignals
valueCues	a matrix of dimensions (number of conditions) * (number of cues), typically CNOlist$valueCues
filename	a name for your file, eg. "plot.pdf"
formalism	New convention is to take the time=0 data set into account to compute the MSE. you can use the previous convetion by setting this argument to something different from the default value.

Details

The coloring of the background is done as follows: the mean absolute difference between observed and simulated values are computed, and colours are chosen based on this value: red (above 0.9), indianred1 (between O.8 and 0.9), lightpink2 (between 0.7 and 0.8), lightpink (between 0.6 and 0.7), mistyrose (between 0.5 and 0.6), palegoldenrod (between 0.4 and 0.5), palegreen (between 0.3 and 0.4), darkolivegreen3 (between 0.2 and 0.3), chartreuse3 (between 0.1 and 0.2), forestgreen (between 0 and 0.1). This function is used inside cutAndPlotResultsT1.

Value

This function doesn't return anything, it just produces a plot in a pdf document in your working directory.

Author(s)

C. Terfve

See Also

plotOptimResults, cutAndPlotResultsT1

Examples

tmpdir<-tempdir()
setwd(tmpdir)

#We will plot the fit of the full initial model compared to the data, without any optimisation
#This is normally not done on a stand alone basis, but if you have a model and would like to visualise 
#its output compared to your data, then this is what you should do

#load and prepare data

data(CNOlistToy,package="CellNOptR")
data(ToyModel,package="CellNOptR")
indicesToy<-indexFinder(CNOlistToy,ToyModel,verbose=TRUE)
ToyFields4Sim<-prep4sim(ToyModel)

#simulate the model

simRes<-simulatorT1(CNOlist=CNOlistToy,model=ToyModel,simList=ToyFields4Sim,indexList=indicesToy)

#format the results and data as expected by plotOptimResults

simResults<-list(t0=matrix(data=0,nrow=dim(simRes)[1],ncol=dim(simRes)[2]),t1=simRes)
expResults<-list(t0=CNOlistToy$valueSignals[[1]],t1=CNOlistToy$valueSignals[[2]])

#plot

plotOptimResultsPDF(
	simResults=simResults,
	expResults=expResults,
	times=CNOlistToy$timeSignals[1:2],
	namesCues=CNOlistToy$namesCues,
	namesSignals=CNOlistToy$namesSignals,
	valueCues=CNOlistToy$valueCues, 
	filename="Toyfull.pdf")

cokelaer/CellNOptR documentation built on May 27, 2019, 8:44 a.m.