--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/DrawSpec.R	Tue Oct 02 12:14:47 2018 -0400
@@ -0,0 +1,74 @@
+drawSpec <- function (X, startP = -1, endP = -1, groupLabel = NULL, useLog = -1, highBound = -1, lowBound = -1, 
+                      xlab = NULL, ylab = NULL, main = NULL, nAxisPos = 4, offside = 0) 
+{
+  groupLabel_name = groupLabel
+  X = as.data.frame(X)
+#  colnames(X) = c(1:ncol(X))
+  X = as.matrix(X)
+  if (highBound != -1) {
+    for (i in 1:nrow(X)) {
+      myIndex = which(X[i, ] > highBound)
+      X[i, myIndex] = highBound
+    }
+  }
+  if (lowBound != -1) {
+    for (i in 1:nrow(X)) {
+      myIndex = which(X[i, ] < lowBound)
+      X[i, myIndex] = lowBound
+    }
+  }
+  if (is.null(groupLabel)) {
+    groupLabel = c(1:nrow(X))
+    groupLabel = as.factor(groupLabel)
+  }
+  else {
+    levels(groupLabel) = c(1:length(levels(groupLabel)))
+  }
+  if (startP == -1) 
+    startP = 1
+  if (endP == -1) 
+    endP = ncol(X)
+  if (is.null(xlab)) {
+    xlab = "index"
+  }
+  if (is.null(ylab)) {
+    ylab = "intensity"
+  }
+  if (is.null(main)) {
+    main = paste(" ", startP + offside, "-", endP + offside)
+  }
+  GraphRange <- c(startP:endP)
+  yn <- X[, GraphRange]
+  if (useLog != -1) 
+    yn = log(yn)
+  if (length(yn) > ncol(X))
+  {
+    plot(yn[1, ], ylim = c(min(yn), max(yn)), type = "n", ylab = ylab, xlab = xlab, main = main, xaxt = "n")
+    tempVal = trunc(length(GraphRange)/nAxisPos)
+    xPos = c(0:nAxisPos) * tempVal
+    axis(1, at = xPos, labels = colnames(X)[xPos + startP + offside])
+    for (i in 1:length(levels(groupLabel))) 
+    {
+      groupLabelIdx = which(groupLabel == levels(groupLabel)[i])
+      color <- palette(rainbow(length(levels(groupLabel))))
+      for (j in 1:length(groupLabelIdx)) 
+      {
+        lines(yn[groupLabelIdx[j], ], col = color[i])
+      }
+    }
+    if (!is.null(groupLabel_name)) 
+    {
+      legendPos = "topleft"
+      legend(legendPos, levels(groupLabel_name), col = as.integer(levels(groupLabel)), text.col = "black", pch = c(19, 19), bg = "gray90")
+    }
+  }
+  if (length(yn) == ncol(X))
+  {
+    plot(yn, ylim = c(min(yn), max(yn)), type = "n", ylab = ylab, xlab = xlab, main = main, xaxt = "n")
+    tempVal = trunc(length(GraphRange)/nAxisPos)
+    xPos = c(0:nAxisPos) * tempVal
+#    axis(1, at = xPos, labels = xPos + startP + offside)
+    axis(1, at = xPos, labels = colnames(X)[xPos + startP + offside])
+    lines(yn)
+  }
+}
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