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# Plots a graph of the transitions in a probabilistic Boolean network.
# <markovSimulation> is the result of a Markov simulation with returnTable=TRUE.
# If stateSubset is specified, only transitions between states in the set are considered.
# If <drawProbabilities> is true, the edges are annotated with probabilities.
# If <drawStateLabels> is true, the states are annotated with their gene values.
# <layout> specifies the igraph layout to be used.
# If <plotIt> is false, only the graph is returned, and nothing is plotted.
# ... specifies further parameters to igraph.
plotPBNTransitions <- function(markovSimulation,stateSubset,
drawProbabilities=TRUE,drawStateLabels=TRUE,
layout=layout.fruchterman.reingold,
plotIt=TRUE,...)
{
stopifnot(inherits(markovSimulation,"MarkovSimulation"))
if (is.null(markovSimulation$table))
stop(paste("The supplied simulation result does not contain transition information.",
"Please re-run markovSimulation() with returnTable=TRUE!"))
# assemble edges from table
edgeMatrix <- data.frame(apply(markovSimulation$table$initialStates,2,
function(x)paste(dec2bin(x,length(markovSimulation$genes)),collapse="")),
apply(markovSimulation$table$nextStates,2,
function(x)paste(dec2bin(x,length(markovSimulation$genes)),collapse="")))
if (!missing(stateSubset))
{
# determine edges to be excluded based on the subset
stateSubset <- sapply(stateSubset,function(x)paste(x,collapse=""))
keepIndices <- apply(edgeMatrix,1,function(row)
{
(length(intersect(row,stateSubset)) == length(unique(row)))
})
# drop edges
edgeMatrix <- edgeMatrix[keepIndices,]
probabilities <- markovSimulation$table$probabilities[keepIndices]
}
else
probabilities <- markovSimulation$table$probabilities
# determine set of vertices
vertices <- as.data.frame(as.character(unique(c(as.character(edgeMatrix[,1]),
as.character(edgeMatrix[,2])))))
# build graph
graph <- graph.data.frame(edgeMatrix,vertices=vertices,directed=TRUE)
if (drawProbabilities)
graph <- set.edge.attribute(graph,"label",value=paste(" ",probabilities))
if (drawStateLabels)
label <- as.character(vertices[,1])
else
label <- NA
if (plotIt)
{
# set default values for further graphical parameters
args <- list(...)
if (is.null(args$vertex.size))
args$vertex.size <- 2
if (is.null(args$edge.arrow.mode))
args$edge.arrow.mode <- 0
if (is.null(args$vertex.label.cex))
args$vertex.label.cex <- 0.75
if (is.null(args$edge.label.cex))
args$edge.label.cex <- 0.75
if (is.null(args$vertex.label.dist))
args$vertex.label.dist <- 1
if (is.null(args$vertex.color))
args$vertex.color <- "grey"
if (is.null(args$edge.label.color))
args$edge.label.color <- "green"
if (is.null(args$edge.arrow.size))
args$edge.arrow.size <- 0.5
# plot it
plot(graph,vertex.label=label,layout=layout,vertex.label.cex=args$vertex.label.cex,
vertex.size=args$vertex.size,vertex.color=args$vertex.color,
vertex.label.dist = args$vertex.label.dist,
edge.arrow.size=args$edge.arrow.size,
edge.label.color=args$edge.label.color,
edge.label.cex=args$edge.label.cex,...)
}
# return the igraph object
return(invisible(graph))
}
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