plotPBNTransitions {BoolNet} | R Documentation |
Visualizes the state transitions and their probabilities in a probabilistic Boolean network. This takes the transition table information calculated by the markovSimulation
method. Only transitions with non-zero probability are included in the plot. The function requires the igraph package.
plotPBNTransitions(markovSimulation, stateSubset, drawProbabilities = TRUE, drawStateLabels = TRUE, layout = layout.fruchterman.reingold, plotIt = TRUE, ...)
markovSimulation |
An object of class |
stateSubset |
An optional list of states, where each element of the list must be a vector with a 0/1 entry for each gene. If this argument is supplied, the graph only contains the specified states and transitions between these states. |
drawProbabilities |
If set to true, the edges of the graph are annotated with the probabilities of the corresponding transitions. Default is TRUE. |
drawStateLabels |
If set to true, the vertices of the graph are annotated with the gene values of the corresponding states. Defaults to TRUE. |
layout |
A layouting function that determines the placement of the nodes in the graph. Please refer to the |
plotIt |
If this is true, a plot is generated. Otherwise, only an object of class |
... |
Further graphical parameters to be passed to |
This function uses the plot.igraph
function from the igraph package. The plots are customizeable using the ...
argument. For details on possible parameters, please refer to igraph.plotting
.
Returns an invisible object of class igraph
containing the wiring graph.
# load example network data(examplePBN) # perform a Markov chain simulation sim <- markovSimulation(examplePBN) # plot the transitions and their probabilities plotPBNTransitions(sim)