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# Custom print function for class TransitionTable
print.TransitionTable <- function(x, activeOnly=FALSE, ...)
{
geneCols <- setdiff(colnames(x),c("attractorAssignment","transitionsToAttractor"))
numGenes <- (length(geneCols)) / 2
colIndices <- c(1,numGenes,numGenes + 1, 2*numGenes);
if ("attractorAssignment" %in% colnames(x))
colIndices <- c(colIndices, 2*numGenes + 1)
if ("transitionsToAttractor" %in% colnames(x))
colIndices <- c(colIndices, 2*numGenes + 2)
genes <- sapply(colnames(x)[seq_len(numGenes)],function(n)strsplit(n,".",fixed=TRUE)[[1]][2])
if(activeOnly)
{
inputStates <- apply(x,1,function(row)
{
r <- paste(genes[which(row[colIndices[1]:colIndices[2]] == 1)],collapse=", ")
if (r == "")
r <- "--"
r
})
outputStates <- apply(x,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(x,1,function(row)
paste(row[colIndices[1]:colIndices[2]],collapse=""))
outputStates <- apply(x,1,function(row)
paste(row[colIndices[3]:colIndices[4]],collapse=""))
colWidth <- numGenes
align <- "right"
}
binMatrix <- cbind(inputStates,outputStates)
if ("attractorAssignment" %in% colnames(x))
binMatrix <- cbind(binMatrix, x[,colIndices[5]])
if ("transitionsToAttractor" %in% colnames(x))
binMatrix <- cbind(binMatrix, x[,colIndices[6]])
binMatrix <- as.data.frame(binMatrix)
cat(format("State",width=max(7,colWidth),justify=align)," ",
format("Next state",width=max(11,colWidth + 2),justify=align),
if ("attractorAssignment" %in% colnames(x))
{
format("Attr. basin",width=13,justify="right")
}
else
"",
if ("transitionsToAttractor" %in% colnames(x))
{
format("# trans. to attr.",width=19,justify="right")
}
else
"",
"\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),
if ("attractorAssignment" %in% colnames(x))
{
format(row[3],width=13,justify="right")
}
else
"",
if ("transitionsToAttractor" %in% colnames(x))
{
format(row[4],width=19,justify="right")
}
else
"",
"\n",sep="")
})
if (!activeOnly)
cat("\nGenes are encoded in the following order: ",
paste(genes,collapse=" "),"\n",sep="")
return(invisible(x))
}
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