Description Usage Arguments Value Author(s) See Also Examples

View source: R/cutAndPlotResultsDT.R

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.

1 2 3 |

`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. |

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

A. MacNamara

plotOptimResultsPan

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 | ```
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
)
``` |

CNORdt documentation built on Nov. 8, 2020, 11:11 p.m.

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