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sequenceToLaTeX <- function(network, startState, includeAttractorStates = c("all","first","none"),
sequence, title="", grouping = list(), plotFixed = TRUE,
onColor="[gray]{0.9}",offColor="[gray]{0.6}", highlightAttractor=TRUE,
reverse=FALSE,
file="sequence.tex")
{
if (!missing(network))
{
stopifnot(inherits(network,"BooleanNetwork") || inherits(network,"SymbolicBooleanNetwork"))
if (missing(startState) || !missing(sequence))
stop("Either \"network\" and \"startState\" or \"sequence\" must be provided!")
sequence <- getPathToAttractor(network = network,
state = startState,
includeAttractorStates = includeAttractorStates)
numGenes <- length(network$genes)
whichFixed <- which(network$fixed != -1)
if (plotFixed | (length(whichFixed) == 0))
plotIndices <- seq_len(numGenes)
else
plotIndices <- seq_len(numGenes)[-whichFixed]
attractor <- attributes(sequence)$attractor
sequence <- sequence[,plotIndices]
attributes(sequence)$attractor <- attractor
}
else
{
if (missing(sequence) || !missing(startState))
stop("Either \"network\" and \"startState\" or \"sequence\" must be provided!")
attractor <- attributes(sequence)$attractor
}
# escape "_" in LaTeX
genes = gsub("_", "\\_", colnames(sequence))
# determine list of genes to be plotted
# Open output file, and print header
sink(file)
cat("% Please include packages tabularx and colortbl in your master document:\n",
"% \\usepackage{tabularx,colortbl}\n\n\n",sep="")
totalMatrix <- t(sequence)
colnames(totalMatrix) <- seq_len(ncol(totalMatrix))
if(length(grouping)>0)
{
# reorder genes according to the supplied groups
totalMatrix <- totalMatrix[unlist(grouping$index),]
separationPositions <- c(1,cumsum(sapply(grouping$index,length)+1))
}
else
separationPositions <- c()
if (highlightAttractor && !is.null(attractor))
{
header <- paste(paste(rep(">{\\centering\\arraybackslash}X",
min(attractor) - 1), collapse = " "),
"|",
paste(rep(">{\\centering\\arraybackslash}X",
length(attractor)), collapse = " "),
"|", sep="")
}
else
header <- paste(rep(">{\\centering\\arraybackslash}X",
ncol(totalMatrix), collapse = " "))
# output table header
cat("\\begin{table}[ht]\n",
"\\begin{center}\n",
"\\caption{",title,"}\n",
"\\begin{tabularx}{\\linewidth}{l",
header,
"}\\hline\n", sep="")
cat("\\textbf{Time}\t&\t",paste(seq_len(ncol(totalMatrix)),collapse="\t&\t"),"\\\\")
if(length(grouping) == 0)
cat("\\hline\n")
else
cat("\n")
# output active and inactive states
if (reverse)
indices <- rev(seq_len(nrow(totalMatrix)))
else
indices <- seq_len(nrow(totalMatrix))
for(j in indices)
{
separator <- which(separationPositions==j)
if (length(separator) != 0)
{
cat("\\hline \\multicolumn{",ncol(totalMatrix) + 1,
"}{c}{",grouping$class[separator],"}\\\\ \\hline \n",sep="")
}
cat("\\textbf{",rownames(totalMatrix)[j],"}\t&\t",sep="")
for(i in seq_len(ncol(totalMatrix)))
{
if(totalMatrix[j,i] == 1)
cat("\\cellcolor",onColor,"1",sep="")
else
cat("\\cellcolor",offColor,"0",sep="")
if (i < ncol(totalMatrix))
cat("\t&\t")
}
cat("\\\\\n")
}
cat("\\hline")
if (highlightAttractor && !is.null(attractor))
{
cat("\\multicolumn{",min(attractor),
"}{c|}{}\t&\t\\multicolumn{",length(attractor),
"}{c|}{Attractor}\\\\\\cline{",min(attractor) + 1, "-", max(attractor) + 1, "}\n",sep="")
}
cat("\\end{tabularx}\n\\end{center}\n",
"\\end{table}\n\n",sep="")
sink()
# return the matrix
return(totalMatrix)
}
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