plotStateGraph {BoolNet} | R Documentation |

## Visualize state transitions and attractor basins

### Description

Plots a graph containing all states visited in `stateGraph`

, and optionally highlights attractors and basins of attraction. This requires the igraph package.

### Usage

```
plotStateGraph(stateGraph, highlightAttractors = TRUE,
colorBasins = TRUE, colorSet,
drawLegend = TRUE, drawLabels = FALSE,
layout = layout.kamada.kawai,
piecewise = FALSE,
basin.lty = 2, attractor.lty = 1,
plotIt = TRUE,
colorsAlpha = c(colorBasinsNodeAlpha = .3,
colorBasinsEdgeAlpha = .3,
colorAttractorNodeAlpha = 1,
colorAttractorEdgeAlpha = 1),
...)
```

### Arguments

`stateGraph` |
An object of class |

`highlightAttractors` |
If this parameter is true, edges in attractors are drawn bold and with a different line type (which can be specified in |

`colorBasins` |
If set to true, each basin of attraction is drawn in a different color. Colors can be specified in |

`colorSet` |
An optional vector specifying the colors to be used for the different attractor basins. If not supplied, a default color set is used. |

`drawLegend` |
If set to true and |

`drawLabels` |
If set to true, the binary encodings of the states are drawn beside the vertices of the graph. As this can be confusing for large graphs, the default value is FALSE. |

`layout` |
A layouting function that determines the placement of the nodes in the graph. Please refer to the |

`piecewise` |
If set to true, a piecewise layout is used, i.e. the subgraphs corresponding to different basins of attraction are separated and layouted separately. |

`basin.lty` |
The line type used for edges in a basin of attraction. Defaults to 2 (dashed). |

`attractor.lty` |
If |

`plotIt` |
If this is true, a plot is generated. Otherwise, only an object of class |

`colorsAlpha` |
These parameters apply alpha correction to the colors of basins and attractors in the following order: basin node, basin edge, attractor node, attractor edge. Defaults to a vector of length 4 with settings |

`...` |
Further graphical parameters to be passed to |

### 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 state graph, including color and line attributes.

### See Also

`getAttractors`

, `simulateSymbolicModel`

, `getTransitionTable`

, `getBasinOfAttraction`

, `getStateSummary`

, `plotNetworkWiring`

, `igraph.plotting`

### Examples

```
# load example data
data(cellcycle)
# get attractors
attractors <- getAttractors(cellcycle)
# plot state graph
## Not run:
plotStateGraph(attractors, main = "Cell cycle network", layout = layout.fruchterman.reingold)
## End(Not run)
```

*BoolNet*version 2.1.9 Index]