plotStateGraph {BoolNet} | R Documentation |
Plots a graph containing all states visited in stateGraph
, and optionally highlights attractors and basins of attraction. This requires the igraph package.
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), ...)
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 |
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 state graph, including color and line attributes.
getAttractors
, simulateSymbolicModel
, getTransitionTable
, getBasinOfAttraction
, getStateSummary
, plotNetworkWiring
, igraph.plotting
# 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)