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cellnopt / CellNOptR

Training of boolean logic models of signalling networks using prior knowledge networks and perturbation data.
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error when calling cutAndPlot variants #14

Open cokelaer opened 9 years ago

cokelaer commented 9 years ago

Got this error:

Error in checkAtAssignment("CNOlist", "stimuli", "numeric") : assignment of an object of class     “numeric” is not valid for @‘stimuli’ in an object of class “CNOlist”; is(value, "matrix") is not TRUE

In this code.

pknmodel = readSIF("PKN.sif") 
d = readMIDAS("test2.csv") 
cnolist = makeCNOlist(d, subfield=FALSE) 
model = preprocessing(cnolist, pknmodel) 
res = gaBinaryT1(cnolist, model, verbose=FALSE)

cutAndPlotResultsT1(model=model, bString=res$bString, CNOlist=cnolist)

cokelaer commented 9 years ago

This is coming from cutandPlotResults when the size of the MIDAS file cannot be plotted on the screen.

Using for instance plotParams=list(maxrow=50) as an argument to cutAndPlot prevents that issue.

This is wierd because we have already handle large MIDAS file before but the fix is to have a more robust cutAndPlot function