R: Plot the wiring of a Boolean network

plotNetworkWiring {BoolNet}

R Documentation

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.

Examples

# load example data
data(cellcycle)

# plot wiring graph
plotNetworkWiring(cellcycle)

[Package BoolNet version 2.1.5 Index]