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# Plot state tables of all attractors in <attractorInfo>.
# Genes are grouped according to <grouping>.
# An additional title can be supplied in <title>.
# If <plotFixed> is set, fixed variables are included in the plot.
# <onColor> and <offColor> specify the colors of ON/1 and OFF/0 states.
# TODO: remove old definition from comments
#plotAttractors <- function (attractorInfo, subset, title = "", mode=c("table","graph"),
# grouping = list(), plotFixed = TRUE, onColor="green",offColor="red",
# layout=layout.circle, drawLabels=TRUE, drawLegend=TRUE, ask=TRUE,
# reverse=FALSE, ...)
#{}
plotAttractors <- function (attractorInfo, subset,
title = "",
mode = c("table", "graph"),
grouping = list(),
plotFixed = TRUE,
onColor = "#4daf4a", offColor = "#e41a1c",
layout = layout.circle,
drawLabels = TRUE, drawLegend = TRUE, ask = TRUE, reverse = FALSE,
# new parameters
borderColor = "black",
eps = 0.1, allInOnePlot = FALSE, ...)
{
stopifnot(inherits(attractorInfo, "AttractorInfo") || inherits(attractorInfo,
"SymbolicSimulation"))
if (inherits(attractorInfo, "AttractorInfo")) {
numGenes <- length(attractorInfo$stateInfo$genes)
geneNames <- attractorInfo$stateInfo$genes
}
else {
numGenes <- ncol(attractorInfo$attractors[[1]])
geneNames <- colnames(attractorInfo$attractors[[1]])
}
if (missing(subset))
subset <- seq_along(attractorInfo$attractors)
else if (any(subset > length(attractorInfo$attractors)))
stop("You specified an attractor index that is greater than the total number of attractors in 'subset'!")
res <- switch(match.arg(mode, c("table", "graph")), table = {
whichFixed <- which(attractorInfo$stateInfo$fixedGenes != -1)
if (plotFixed | (length(whichFixed) == 0)) {
plotIndices <- seq_len(numGenes)
} else {
plotIndices <- seq_len(numGenes)[-whichFixed]
}
if (inherits(attractorInfo, "AttractorInfo")) {
binMatrices <- lapply(attractorInfo$attractors, function(attractor) {
res <- matrix(apply(attractor$involvedStates, 2, function(state) dec2bin(state, numGenes)[plotIndices]), nrow = length(plotIndices))
})
attractorLengths <- sapply(attractorInfo$attractors, function(attractor) {
ifelse (is.null(attractor$initialStates), ncol(attractor$involvedStates), -1)
})
} else {
binMatrices <- lapply(attractorInfo$attractors, t)
attractorLengths <- sapply(binMatrices, ncol)
}
lengthTable <- table(attractorLengths)
lengthTable <- lengthTable[as.integer(names(lengthTable)) != -1]
oldAsk <- par("ask")
oldmfrow <- NULL
if (allInOnePlot) {
oldmfrow <- par()$mfrow
#par(mfrow=c(1,length(table(sapply(sapply(attractorInfo$attractors, "[[", "involvedStates", simplify=F), ncol)))))
par(mfrow=c(1,length(lengthTable)))
}
res <- lapply(seq_along(lengthTable), function(i) {
len <- as.integer(names(lengthTable)[i])
attractorIndices <- intersect(which(attractorLengths == len), subset)
if (length(attractorIndices) > 0) {
cnt <- length(attractorIndices)
totalMatrix <- c()
for (mat in binMatrices[attractorIndices]) {
totalMatrix <- cbind(totalMatrix, mat)
}
rownames(totalMatrix) <- geneNames[plotIndices]
colnames(totalMatrix) <- sapply(attractorIndices, function(i) paste("Attr", i, ".", seq_len(len), sep = ""))
if (length(grouping) > 0) totalMatrix <- totalMatrix[unlist(grouping$index), , drop = FALSE]
par(ask = ask && i > 1 && dev.interactive())
if (reverse) {
plot(c(), c(),
xlim = c(0, len *cnt), ylim = c(-2, nrow(totalMatrix) + 1),
xlab = "", ylab = "", axes = FALSE,
main = paste(title, "\nAttractors with ", len, " state(s)", sep = ""))
} else {
plot(c(), c(),
xlim = c(0, len * cnt), ylim = c(nrow(totalMatrix) + 1, -2),
xlab = "", ylab = "", axes = FALSE,
main = paste(title, "\nAttractors with ", len," state(s)", sep = ""))
}
#rect(par("usr")[1], par("usr")[3], par("usr")[2], par("usr")[4], col = "grey")
axis(2, seq_len(nrow(totalMatrix)) - 0.5, rownames(totalMatrix), yaxt = "s", las = 2)
xStart <- 1
unitFactor <- (len - (2 * eps))/len
startX <- eps
for (i in seq_len(ncol(totalMatrix))) {
for (j in seq_len(nrow(totalMatrix))) {
rectCol <- ifelse(totalMatrix[j, i], onColor, offColor)
rect(startX, j - 1, startX + unitFactor, j, col = rectCol, border = borderColor, lwd = 2)
}
startX <- startX + unitFactor
if (i %% len == 0) {
startX <- startX + 2*eps
}
}
sep = seq(0, ncol(totalMatrix), by = len)
#abline(v = sep[-1], col = par()$bg, lwd = 3)
if (inherits(attractorInfo, "AttractorInfo")) {
if (is.null(attractorInfo$stateInfo$table)) {
freq <- rep(NA, length(attractorIndices))
}
else {
freq <- round(100 * sapply(attractorInfo$attractors[attractorIndices], function(attractor) {
attractor$basinSize/ncol(attractorInfo$stateInfo$table)}), 2)
}
} else {
if (!is.null(attractorInfo$graph)) {
freq <- round(sapply(attractorIndices, function(i) sum(attractorInfo$graph$attractorAssignment == i)/nrow(attractorInfo$graph)) * 100, 2)
} else {
freq <- rep(NA, length(attractorIndices))
}
}
if (!isTRUE(all(is.na(freq)))) {
text(sep[seq_along(sep) - 1] + len/2, ifelse(reverse, -nrow(totalMatrix)-1.5, 1) + rep(1 + nrow(totalMatrix), ncol(totalMatrix)), paste(freq, "%", sep = ""), cex = 0.75, font = 3)
}
if (length(grouping) > 0) {
if(!is.null(grouping$class)) {
sepPos = cumsum(sapply(grouping$index, length))
abline(h = sepPos[-length(sepPos)], col = "black", lwd = 3)
text(ncol(totalMatrix)/2, sepPos - 0.5, grouping$class, cex = 0.9)
}
}
#if (drawLegend) legend(x = "bottomright", pch = c(15, 15), col = c(onColor, offColor), legend = c("active", "inactive"), cex = 0.7, horiz = T, xpd = T)
if (drawLegend) legend(x = 0, y = ifelse(reverse, -nrow(totalMatrix)-1, 2) + nrow(totalMatrix), pch = c(15, 15), col = c(onColor, offColor), legend = c("active", "inactive"), cex = 0.7, horiz = T, xpd=T)
totalMatrix
}
})
par(ask = oldAsk)
if(!is.null(oldmfrow)) par(mfrow = oldmfrow)
names(res) <- names(lengthTable)
return(res)
}, graph = {
args <- list(...)
if (is.null(args$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$vertex.label.cex <- 0.75
if (is.null(args$vertex.label.dist)) args$vertex.label.dist <- 1
if (is.null(args$vertex.color)) args$vertex.color <- "grey"
if (is.null(args$edge.arrow.size)) args$edge.arrow.size <- 0.5
lapply(attractorInfo$attractors[subset], function(attractor) {
if (inherits(attractorInfo, "AttractorInfo")) {
nodes <- data.frame(apply(attractor$involvedStates, 2, function(state) paste(dec2bin(state, numGenes), collapse = "")), stringsAsFactors = FALSE)
if (!is.null(attractor$initialStates)) {
initialStates <- apply(attractor$initialStates, 2, function(state) paste(dec2bin(state, numGenes), collapse = ""))
nextStates <- apply(attractor$nextStates, 2, function(state) paste(dec2bin(state, numGenes), collapse = ""))
} else {
initialStates <- apply(attractor$involvedStates, 2, function(state) paste(dec2bin(state, numGenes), collapse = ""))
if (length(initialStates) == 1) nextStates <- initialStates else nextStates <- initialStates[c(2:length(initialStates), 1)]
}
} else {
initialStates <- apply(attractor, 1, paste, collapse = "")
nextStates <- apply(attractor[c(2:nrow(attractor), 1), , drop = FALSE], 1, paste, collapse = "")
nodes <- data.frame(unique(c(initialStates, nextStates)), stringsAsFactors = FALSE)
}
edgeMatrix <- data.frame(initialStates, nextStates)
graph <- graph.data.frame(edgeMatrix, vertices = nodes, directed = TRUE)
if (drawLabels) labels <- nodes[, 1] else labels <- NA
args$layout <- layout
args$x <- graph
args$vertex.label <- labels
args$main <- title
do.call("plot", args)
graph
})
})
}
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