Nothing
# Custom print function for class MarkovSimulation
print.MarkovSimulation <- function(x, activeOnly = FALSE, ...)
{
genes <- x$genes
numGenes <- length(genes)
cat("States reached at the end of the simulation:\n")
if (activeOnly)
{
reachedStates <- data.frame(apply(x$reachedStates[,seq_len(numGenes)],1,function(state)
{
r <- paste(genes[which(state == 1)],collapse=", ")
if (r == "")
r <- "--"
r
}),x$reachedStates$Probability)
colnames(reachedStates) <- c("Active genes", "Probability")
print(reachedStates)
}
else
{
print(x$reachedStates)
}
if (!is.null(x$table))
{
cat("\nProbabilities of state transitions in the network:\n")
transitionProbs <- getTransitionProbabilities(x)
colIndices <- c(1,numGenes,numGenes + 1, 2*numGenes,
2*numGenes + 1)
if(activeOnly)
{
inputStates <- apply(transitionProbs,1,function(row)
{
r <- paste(genes[which(row[colIndices[1]:colIndices[2]] == 1)],collapse=", ")
if (r == "")
r <- "--"
r
})
outputStates <- apply(transitionProbs,1,function(row)
{
r <- paste(genes[which(row[colIndices[3]:colIndices[4]] == 1)],collapse=", ")
if (r == "")
r <- "--"
r
})
colWidth <- max(c(sapply(inputStates,nchar),sapply(outputStates,nchar)))
align <- "left"
}
else
{
inputStates <- apply(transitionProbs,1,function(row)
paste(row[colIndices[1]:colIndices[2]],collapse=""))
outputStates <- apply(transitionProbs,1,function(row)
paste(row[colIndices[3]:colIndices[4]],collapse=""))
colWidth <- numGenes
align <- "right"
}
binMatrix <- data.frame(inputStates,outputStates,
transitionProbs[,colIndices[5]])
cat(format("State",width=max(7,colWidth),justify=align)," ",
format("Next state",width=max(11,colWidth + 2),justify=align),
format("Probability",width=13,justify="right"),"\n",sep="")
apply(binMatrix,1,function(row)
{
# paste all states of input and output into one string, and put out all columns of the table in a
# formatted way
cat(format(row[1],width=max(7,colWidth),justify=align),
" => ",
format(row[2],width=max(11,colWidth + 2),justify=align),
format(row[3],width=13,justify="right"),"\n",sep="")
})
}
return(invisible(x))
}
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