DrawSpec.R

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)
    }
}