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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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