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Created February 2, 2016 14:29
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  1. @invalid-email-address Anonymous created this gist Feb 2, 2016.
    85 changes: 85 additions & 0 deletions Example code
    View file
    Original file line number Diff line number Diff line change
    @@ -0,0 +1,85 @@
    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>