plotNetworkWiring: Plot the wiring of a Boolean network

In BoolNet: Construction, Simulation and Analysis of Boolean Networks

Plot the wiring of a Boolean network

Description

Plots the wiring of genes (i.e. the gene dependencies) of a synchronous or probabilistic Boolean network. The nodes of the graph are the genes, and the directed edges show the dependencies of the genes. This requires the igraph package.

Usage

plotNetworkWiring(network, 
                  layout = layout.fruchterman.reingold, 
                  plotIt = TRUE, ...)

Arguments

network	A network structure of class BooleanNetwork, SymbolicBooleanNetwork or ProbabilisticBooleanNetwork. These networks can be read from files by loadNetwork, generated by generateRandomNKNetwork, or reconstructed by reconstructNetwork.
layout	A layouting function that determines the placement of the nodes in the graph. Please refer to the layout manual entry in the igraph package for further details. By default, the Fruchterman-Reingold algorithm is used.
plotIt	If this is true, a plot is generated. Otherwise, only an object of class igraph is returned, but no plot is drawn.
...	Further graphical parameters to be passed to plot.igraph.

Details

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.

Value

Returns an invisible object of class igraph containing the wiring graph.

See Also

loadNetwork, generateRandomNKNetwork, reconstructNetwork, plotStateGraph, igraph.plotting

Examples

## Not run: 
# load example data
data(cellcycle)

# plot wiring graph
plotNetworkWiring(cellcycle)

## End(Not run)

BoolNet documentation built on Oct. 2, 2023, 5:08 p.m.