R/dart.R

In yufree/dartms: Direct Analysis in Real Time (DART) Mass Spectrometry Data Analysis

#' plot dart ms data
#' @param data matrix with row mz, column rt and cell intensity
#' @param inscf intensity cutoff in Log scale
#' @return NULL
#' @export
plotmz <- function(data, inscf = 5, ...) {
        mz <- as.numeric(rownames(data))
        rt <- as.numeric(colnames(data))
        z <- log10(data + 1)
        cex = as.numeric(cut(z - inscf, breaks = c(0, 1, 2, 3, 4, Inf) /
                                     2)) / 2
        cexlab = c(
                paste0(inscf, '-', inscf + 0.5),
                paste0(inscf + 0.5, '-', inscf + 1),
                paste0(inscf + 1, '-', inscf + 1.5),
                paste0(inscf + 1.5, '-', inscf + 2),
                paste0('>', inscf + 2)
        )

        z[z < inscf] <- NA
        corr <- which(!is.na(z), arr.ind = TRUE)
        mz0 <- mz[corr[, 1]]
        rt0 <- rt[corr[, 2]]
        int <- z[which(!is.na(z))]

        par(mar=c(5, 4.2, 6.1, 2.1), xpd=TRUE)
        graphics::plot(
                mz0 ~ rt0,
                pch = 19,
                cex = cex,
                col = grDevices::rgb(0, 0, 1, 0.1),
                xlab = "retention time(s)",
                ylab = "m/z",
                ...
        )
        graphics::legend(
                'top',
                legend = cexlab,
                title = 'Intensity in Log scale',
                pt.cex = c(1,2,3,4,5)/2,
                pch = 19,
                bty = 'n',
                horiz = T,
                cex = 0.7,
                col = grDevices::rgb(0, 0, 1, 0.1),
                inset = c(0, -0.25)

        )
}

#' plot dart ms data
#' @param file mzxml file path
#' @param profstep step size (in m/z) to use for profile generation, default 0.1
#' @param inscf intensity cutoff in Log scale
#' @return NULL
#' @export
plotdart <- function(file,inscf, profstep = 0.1){
    data <- xcms::xcmsRaw(file,profstep = profstep)
        pf <- xcms::profMat(data)
        rownames(pf) <- mz <- xcms::profMz(data)
        colnames(pf) <- rt <- data@scantime
        plotmz(pf,inscf = inscf)
}
#' plot average dart ms data as Mass Spectrum
#' @param file mzxml file path
#' @param profstep step size (in m/z) to use for profile generation, default 0.1
#' @return NULL
#' @export
plotdartms <- function(file,profstep = 0.1){
    data <- xcms::xcmsRaw(file,profstep = profstep)
        pf <- xcms::profMat(data)
        rownames(pf) <- mz <- xcms::profMz(data)
        colnames(pf) <- rt <- data@scantime
        mzins <- apply(pf,1,sum)/length(unique(rt))
        plot(mzins~mz, xlab = 'm/z',ylab = 'intensity',type = 'h',main = 'Mass Spectrum')
}