R/ms2_plot.R

In tidymass/tinytools: All the usefull tools for MS data processing and analysis

#' @title ms2_plot2
#' @description Plot ms2 spectra or ms2 match plot.
#' @author Xiaotao Shen
#' \email{shenxt1990@@outlook.com}
#' @param spectrum1 Spectrum 1.
#' @param spectrum2 Spectrum 2.
#' @param spectrum1_name Name of spectrum1
#' @param spectrum2_name Name of spectrum2
#' @param range.mz range.mz
#' @param ppm.tol ppm.tol
#' @param mz.ppm.thr mz.ppm.thr
#' @param xlab xlab.
#' @param ylab ylab.
#' @param col1 Color 1.
#' @param col2 Color 2.
#' @param title.size title.size
#' @param lab.size lab.size
#' @param axis.text.size axis.text.size.
#' @param legend.title.size legend.title.size
#' @param legend.text.size legend.text.size
#' @param interactive_plot Interactive plot or not.
#' @return Return a MS2 spectrum.
#' @export
#' @examples
#' spectrum1 <- data.frame(
#'     mz = c(
#'         87.50874,
#'         94.85532,
#'         97.17808,
#'         97.25629,
#'         103.36186,
#'         106.96647,
#'         107.21461,
#'         111.00887,
#'         113.79269,
#'         118.70564
#'     ),
#'     intensity =
#'         c(
#'             8356.306,
#'             7654.128,
#'             9456.207,
#'             8837.188,
#'             8560.228,
#'             8746.359,
#'             8379.361,
#'             169741.797,
#'             7953.080,
#'             8378.066
#'         )
#' )
#' spectrum2 <- spectrum1
#' ms2_plot(spectrum1, spectrum2)
#' ms2_plot(spectrum1, spectrum2, interactive_plot = TRUE)
#' ms2_plot(spectrum1)
#' ms2_plot(spectrum1, interactive_plot = TRUE)
ms2_plot <- function(spectrum1,
                     spectrum2,
                     spectrum1_name = "spectrum1",
                     spectrum2_name = "spectrum2",
                     range.mz,
                     ppm.tol = 30,
                     mz.ppm.thr = 400,
                     xlab = "Mass to charge ratio (m/z)",
                     ylab = "Relative intensity",
                     col1 = "red",
                     col2 = "black",
                     title.size = 15,
                     lab.size = 15,
                     axis.text.size = 15,
                     legend.title.size = 15,
                     legend.text.size = 15,
                     interactive_plot = FALSE) {
    if (missing(spectrum1) & missing(spectrum2)) {
        stop("No spectrum1 and spectrum2")
    }
    if (!missing(spectrum1)) {
        spectrum1 <-
            apply(spectrum1, 2, function(x) {
                as.numeric(x)
            }) %>%
            as.data.frame()

        spectrum1[, 2] <- spectrum1[, 2] / max(spectrum1[, 2])
    }

    if (!missing(spectrum2)) {
        spectrum2 <-
            apply(spectrum2, 2, function(x) {
                as.numeric(x)
            }) %>%
            as.data.frame()
        spectrum2[, 2] <- spectrum2[, 2] / max(spectrum2[, 2])
    }

    ## two spectrum
    if (!missing(spectrum1) & !missing(spectrum2)) {
        if (missing(range.mz)) {
            range.mz <- c(
                min(spectrum1[, 1], spectrum2[, 1]),
                max(spectrum1[, 1], spectrum2[, 1])
            )
        }

        matched.spec <- ms2Match(spectrum1,
            spectrum2,
            ppm.tol = ppm.tol,
            mz.ppm.thr = mz.ppm.thr
        )

        matched.idx <- which(matched.spec[, "Lib.intensity"] > 0 &
            matched.spec[, "Exp.intensity"] > 0)

        plot <- ggplot(matched.spec) +
            geom_segment(
                mapping = aes(
                    x = Exp.mz,
                    y = Exp.intensity - Exp.intensity,
                    xend = Exp.mz,
                    yend = Exp.intensity
                ),
                colour = col2
            ) +
            geom_point(
                data = matched.spec[matched.idx, , drop = FALSE],
                mapping = aes(x = Exp.mz, y = Exp.intensity),
                colour = col2
            ) +
            xlim(range.mz[1], range.mz[2]) +
            labs(x = xlab, y = ylab) +
            scale_y_continuous(
                limits = c(-1, 1),
                breaks = c(-1, -0.5, 0, 0.5, 1),
                labels = c("1", "0.5", "0", "0.5", "1")
            ) +
            theme_bw() +
            theme(
                # axis.line = element_line(arrow = arrow()),
                plot.title = element_text(
                    color = "black",
                    size = title.size,
                    face = "plain",
                    hjust = 0.5
                ),
                axis.title = element_text(
                    color = "black",
                    size = lab.size,
                    face = "plain"
                ),
                axis.text = element_text(
                    color = "black",
                    size = axis.text.size,
                    face = "plain"
                ),
                legend.title = element_text(
                    color = "black",
                    size = legend.title.size,
                    face = "plain"
                ),
                legend.text = element_text(
                    color = "black",
                    size = legend.text.size,
                    face = "plain"
                )
            )

        plot <- plot +
            annotate(
                geom = "text",
                x = Inf,
                y = Inf,
                label = spectrum1_name,
                color = col2,
                hjust = 1,
                vjust = 1
            ) +
            annotate(
                geom = "text",
                x = Inf,
                y = -Inf,
                label = spectrum2_name,
                color = col1,
                hjust = 1,
                vjust = -1
            )

        plot <- plot +
            geom_segment(
                data = matched.spec,
                mapping = aes(
                    x = Lib.mz,
                    y = Lib.intensity - Lib.intensity,
                    xend = Lib.mz,
                    yend = -Lib.intensity
                ),
                colour = col1
            ) +
            geom_point(
                data = matched.spec[matched.idx, , drop = FALSE],
                mapping = aes(x = Lib.mz, y = -Lib.intensity),
                colour = col1
            )
        if (interactive_plot) {
            plot <- plotly::ggplotly(plot)
        }
        return(plot)
    }

    if (!missing(spectrum1) & missing(spectrum2)) {
        spectrum <- spectrum1
    }

    if (!missing(spectrum2) & missing(spectrum1)) {
        spectrum <- spectrum2
    }

    if (missing(range.mz)) {
        range.mz <- c(min(spectrum[, 1]), max(spectrum[, 1]))
    }

    plot <- ggplot(spectrum) +
        geom_segment(
            mapping = aes(
                x = mz,
                y = 0,
                xend = mz,
                yend = intensity
            ),
            colour = col1
        ) +
        xlim(range.mz[1], range.mz[2]) +
        labs(x = xlab, y = ylab) +
        scale_y_continuous(expand = expansion(mult = c(0, 0.1))) +
        theme_bw() +
        theme(
            # axis.line = element_line(arrow = arrow()),
            plot.title = element_text(
                color = "black",
                size = title.size,
                face = "plain",
                hjust = 0.5
            ),
            axis.title = element_text(
                color = "black",
                size = lab.size,
                face = "plain"
            ),
            axis.text = element_text(
                color = "black",
                size = axis.text.size,
                face = "plain"
            ),
            legend.title = element_text(
                color = "black",
                size = legend.title.size,
                face = "plain"
            ),
            legend.text = element_text(
                color = "black",
                size = legend.text.size,
                face = "plain"
            )
        )

    if (interactive_plot) {
        plot <- plotly::ggplotly(plot)
    }
    plot
}