| Previous changeset 6:d4e56ce4485e (2017-03-02) Next changeset 8:c54c70af216b (2017-04-20) |
|
Commit message:
Uploaded |
|
added:
nmr_bucketing/DrawSpec.R |
| b |
| diff -r d4e56ce4485e -r 1df0b8efe9fc nmr_bucketing/DrawSpec.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/nmr_bucketing/DrawSpec.R Mon Mar 06 06:34:01 2017 -0500 |
| [ |
| @@ -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) + } +} \ No newline at end of file |