February 2, 2016 14:29 · Feb 2, 2016
diff --git a/Example code b/Example code
@@ -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>