plotModelSimulation: Plot the predictions by the model

Description Usage Arguments Value Author(s)

Description

Plot the predictions by the model

Usage

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plotModelSimulation(model_description, targets = "all", readouts = "all",
  inhibition_effect = NA, log_axis = TRUE, with_data = FALSE,
  compare = list())

Arguments

model_description

A MRAmodel object that describes the model to be fitted

targets

A matrix of perturbations to simulate, as generated by getCombinationMatrix or "all" to reproduce the perturbations used to build the model A perturbation matrix is filled with 0 and 1, each row is a perturbation set and column names are used to determine the name of the perturbation.

readouts

List of nodes to simulate. If "all", all the nodes measured to fit the model will be used. Only nodes actually measured or inhibited for the model can be simulated.

inhibition_effect

A single value, a list of values or NA. Values in ]0, -inf] to use for the inhibition, representing the log2-fold change in activity of the node (alternatively, a value between 0 and 1 representing the fraction of activity remaining after inhibition compared to basal). If NA, the values fitted for the inhibition will be used, or -1 if an inhibition is requested for a node that was not inhibited in the experiment.

log_axis

Boolean, whether the ordinate axis should be in log scale

with_data

Plot the data of the model next to the prediction

compare

A list of MRAmodel to compare the predictions, targets and readouts must be valid for MRAmodels

Value

A list that represents a MIDAS measure-like format with fields 'conditions' the matrix of perturbations provided as 'targets', 'bestfit' the simulation, and 'variants' a list of simulations for the alternative parameter sets from profile likelihood

Invisibly, the matrix of the results of the simulation

Author(s)

Mathurin Dorel mathurin.dorel@charite.de


MathurinD/STASNet documentation built on May 28, 2019, 1:50 p.m.