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function (eset, cl, mfrow = c(1, 1), colo, min.mem = 0, time.labels,
new.window = TRUE)
{
clusterindex <- cl[[3]]
memship <- cl[[4]]
memship[memship < min.mem] <- -1
colorindex <- integer(dim(exprs(eset))[[1]])
if (missing(colo)) {
colo <- c("#FF8F00", "#FFA700", "#FFBF00", "#FFD700",
"#FFEF00", "#F7FF00", "#DFFF00", "#C7FF00", "#AFFF00",
"#97FF00", "#80FF00", "#68FF00", "#50FF00", "#38FF00",
"#20FF00", "#08FF00", "#00FF10", "#00FF28", "#00FF40",
"#00FF58", "#00FF70", "#00FF87", "#00FF9F", "#00FFB7",
"#00FFCF", "#00FFE7", "#00FFFF", "#00E7FF", "#00CFFF",
"#00B7FF", "#009FFF", "#0087FF", "#0070FF", "#0058FF",
"#0040FF", "#0028FF", "#0010FF", "#0800FF", "#2000FF",
"#3800FF", "#5000FF", "#6800FF", "#8000FF", "#9700FF",
"#AF00FF", "#C700FF", "#DF00FF", "#F700FF", "#FF00EF",
"#FF00D7", "#FF00BF", "#FF00A7", "#FF008F", "#FF0078",
"#FF0060", "#FF0048", "#FF0030", "#FF0018")
}
colorseq <- seq(0, 1, length = length(colo))
for (j in 1:max(clusterindex)) {
tmp <- exprs(eset)[clusterindex == j, ]
tmpmem <- memship[clusterindex == j, j]
if (((j - 1)%%(mfrow[1] * mfrow[2])) == 0) {
if (new.window)
X11()
par(mfrow = mfrow)
if (sum(clusterindex == j) == 0) {
ymin <- -1
ymax <- +1
}
else {
ymin <- min(tmp)
ymax <- max(tmp)
}
plot.default(x = NA, xlim = c(1, dim(exprs(eset))[[2]]),
ylim = c(ymin, ymax), xlab = "Time", ylab = "Expression changes",
main = paste("Cluster", j), axes = FALSE)
if (missing(time.labels)) {
axis(1, 1:dim(exprs(eset))[[2]], c(1:dim(exprs(eset))[[2]]))
axis(2)
}
else {
axis(1, 1:dim(exprs(eset))[[2]], time.labels)
axis(2)
}
}
else {
if (sum(clusterindex == j) == 0) {
ymin <- -1
ymax <- +1
}
else {
ymin <- min(tmp)
ymax <- max(tmp)
}
plot.default(x = NA, xlim = c(1, dim(exprs(eset))[[2]]),
ylim = c(ymin, ymax), xlab = "Time", ylab = "Expression changes",
main = paste("Cluster", j), axes = FALSE)
if (missing(time.labels)) {
axis(1, 1:dim(exprs(eset))[[2]], c(1:dim(exprs(eset))[[2]]))
axis(2)
}
else {
axis(1, 1:dim(exprs(eset))[[2]], time.labels)
axis(2)
}
}
if (!(sum(clusterindex == j) == 0)) {
for (jj in 1:(length(colorseq) - 1)) {
tmpcol <- (tmpmem >= colorseq[jj] & tmpmem <=
colorseq[jj + 1])
if (sum(tmpcol) > 0) {
tmpind <- which(tmpcol)
for (k in 1:length(tmpind)) {
lines(tmp[tmpind[k], ], col = colo[jj])
}
}
}
}
}
}
<environment: namespace:Mfuzz>
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