R/plotRidgeList.R

In zeehio/MassSpecWavelet: Peak Detection for Mass Spectrometry data using wavelet-based algorithms

#' Plot the ridge list
#'
#' Plot the ridge list returned by [getRidge()]
#'
#'
#' @param ridgeList returned by [getRidge()]
#' @param wCoefs 2-D CWT coefficients
#' @param range plot range of m/z index
#' @param colorMap colorMap to plot the points of local maximum
#' @param main parameter of [plot()]
#' @param pch parameter of [plot()]
#' @param cex parameter of [plot()]
#' @param \dots other parameters of [points()]
#' @return No value is returned; this function is called for its side effects
#' (plot).
#' @author Pan Du
#' @seealso [getRidge()]
#' @keywords hplot
#' @export
#' @examples
#'
#' data(exampleMS)
#' scales <- seq(1, 64, 3)
#' wCoefs <- cwt(exampleMS[5000:11000], scales = scales, wavelet = "mexh")
#'
#' localMax <- getLocalMaximumCWT(wCoefs)
#' ridgeList <- getRidge(localMax)
#' plotRidgeList(ridgeList)
#'
plotRidgeList <- function(ridgeList, wCoefs = NULL, range = NULL, colorMap = "RYB", main = NULL, pch = ".", cex = 3, ...) {
    if (colorMap == "RYB") {
        rgb.palette <- grDevices::colorRampPalette(c("red", "orange", "blue"),
            space = "rgb"
        )
        colorMap <- rgb.palette(255)
        # colorMap <- heat.colors(255)
    }
    ridgeLen <- vapply(ridgeList, length, integer(1L))
    ridgeName <- names(ridgeList)
    ridgeInfo <- matrix(as.numeric(unlist(strsplit(ridgeName, "_"))), nrow = 2)
    ridgeLevel <- ridgeInfo[1, ]
    mzInd <- ridgeInfo[2, ]

    scales <- attr(ridgeList, "scales")
    if (is.null(scales)) scales <- 0:max(ridgeLen)
    ## Check range parameter
    if (!is.null(range)) {
        range <- sort(range)
        if (length(range) == 1) range <- c(range, max(mzInd))
        if (range[1] < 1) range[1] <- 1
        if (range[2] > max(mzInd)) range[2] <- max(mzInd)
    } else {
        range <- c(1, max(mzInd))
    }

    selInd <- which(mzInd >= range[1] & mzInd <= range[2])
    selMzInd <- mzInd[selInd]
    selRidgeList <- ridgeList[selInd]
    selRidgeLen <- ridgeLen[selInd]
    selRidgeLevel <- ridgeLevel[selInd]

    plot(seq(range[1], range[2], length = length(scales)), scales, type = "n", xlab = "m/z index", ylab = "CWT coefficient scale", main = main)
    if (!is.null(wCoefs)) {
        if (length(scales) != ncol(wCoefs)) stop('The length of "scales" does not match with "wCoefs"!')
        # if (!is.null(skip)) {
        #     wCoefs <- wCoefs[, -skip]
        # }
        range <- round(range)
        maxSelV <- max(wCoefs[range[1]:range[2], ])
    }

    for (i in 1:length(selMzInd)) {
        ridge.i <- selRidgeList[[i]]
        level.i <- selRidgeLevel[i]
        levels.i <- level.i:(level.i + selRidgeLen[i] - 1)
        scales.i <- scales[levels.i]

        if (is.null(wCoefs)) {
            col <- "blue"
        } else {
            coefInd.i <- cbind(ridge.i, levels.i)
            ridgeValue.i <- wCoefs[coefInd.i]
            col <- colorMap[1 + log(1 + abs(ridgeValue.i)) * 255 / log(1 + maxSelV)]
        }
        graphics::points(ridge.i, scales.i, pch = pch, cex = cex, col = col, ...)
    }
}