cutAndPlotResultsDT: Plot the results of a time-course optimization

In saezlab/CNORdt: Add-on to CellNOptR: Discretized time treatments

Description

This function takes the optimized bit string, cuts the model according to the string and then finds the optimized scaling factor to pass on to plotOptimResultsPan for visualization.

Usage

cutAndPlotResultsDT(model, bString, simList=NULL, CNOlist, indexList=NULL,
plotPDF=FALSE, tag=NULL, plotParams=list(maxrow=10), boolUpdates=boolUpdates,
lowerB=lowerB, upperB=upperB, sizeFac = 1e-04, NAFac = 1)

Arguments

model	The expanded model used as input for gaBinaryDT.
bString	A bit string as output by gabinaryDT (i.e. a vector of 1s and 0s).
simList	A simlist corresponding to the model, as output by prep4sim.
CNOlist	The CNOlist used in optimization.
indexList	An indexList, produced by indexFinder run on the model and the CNOlist above.
plotPDF	TRUE or FALSE; for pdf output.
tag	NULL or string; prefixes filenames with a tag (replaces the default behavior).
plotParams	A list of options related to the PDF and plotting outputs. (1) maxrow is the maximum number of rows used to plot the results. See plotOptimResultsPan for other fields.
boolUpdates	The number of synchronous updates performed by the boolean simulator.
lowerB	The lower bound for the optimized value of the scaling factor.
upperB	The upper bound for the optimized value of the scaling factor.
sizeFac	The scaling factor for the size term in the objective function, default to 0.0001.
NAFac	The scaling factor for the NA term in the objective function, default to 1.

Value

This function doesn't return anything, it only plots the graph in your graphic window.

Author(s)

A. MacNamara

See Also

plotOptimResultsPan

Examples

data(CNOlistPB, package="CNORdt")
data(modelPB, package="CNORdt")

# pre-process model
model <- preprocessing(CNOlistPB, modelPB)
indices = indexFinder(CNOlistPB, model)
fields4Sim <- prep4sim(model=model)
initBstring <- rep(1, length(model$reacID))

# optimize
opt1 <- gaBinaryDT(CNOlist=CNOlistPB, model=model, initBstring=initBstring,
verbose=TRUE, boolUpdates=10, maxTime=30, lowerB=0.8, upperB=10)

cutAndPlotResultsDT(
  model=model,
  CNOlist=CNOlistPB,
  bString=opt1$bString,
  plotPDF=FALSE,
  boolUpdates=10,
  lowerB=0.8, 
  upperB=10
)

saezlab/CNORdt documentation built on May 17, 2019, 1:59 p.m.