Description Usage Arguments Value Author(s)
View source: R/simulation_model.R
Plot the predictions by the model
1 2 3 | plotModelSimulation(model_description, targets = "all",
readouts = "all", inhibition_effect = NA, log_axis = TRUE,
with_data = FALSE, compare = list())
|
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 |
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
Mathurin Dorel mathurin.dorel@charite.de
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