R/plots.R

In hadexversum/powerHDX: Efficient Simulation of HDX-MS Data and Tools for the Statistical Analysis

#' Draw mass spectra
#'
#' @description Graphical visualization of mass spectra obtained using the
#' function \code{\link[powerHaDeX]{simulate_theoretical_spectra}}.
#'
#' @param spectra data table. Result of
#' \code{\link[powerHaDeX]{simulate_theoretical_spectra}}.
#' @param time_points vector of values of exposure times to be displayed on the
#' plot. Default \code{unique(spectra[["Exposure"]])}.
#' @param charges vector of charges to be displayed on the plot. Default
#' \code{unique(spectra[["Charge"]])}.
#' @param control_time logical. Indicates whether the spectrum at the control
#' time (conventionally equal to 0) should be drawn.
#' @param ... additional arguments passing to the \code{\link[ggplot2]{theme}}.
#'
#' @return ggplot object
#'
#' @details This function draws mass spectra from data obtained via
#' \code{\link[powerHaDeX]{simulate_theoretical_spectra}}.
#'
#' @examples
#'
#' theo_spectra <- simulate_theoretical_spectra(sequence = "LVRKDLQN",
#'                                              charge = c(3, 5),
#'                                              protection_factor = 100,
#'                                              times = c(0.167, 5),
#'                                              pH = 7.5,
#'                                              temperature = 15,
#'                                              n_molecules = 500,
#'                                              time_step_const = 1,
#'                                              use_markov = TRUE)
#'
#' plot_spectra(theo_spectra)
#'
#' @export


plot_spectra <- function(spectra,
                         time_points = unique(spectra[["Exposure"]]),
                         charges = unique(spectra[["Charge"]]),
                         control_time = FALSE,
                         ...) {

    Mz <- Intensity <- NULL

    if(control_time) {

        spectra <- spectra[spectra[["Exposure"]] %in% time_points &
                               spectra[["Charge"]] %in% charges]
    }else{

        spectra <- spectra[spectra[["Exposure"]] %in% time_points &
                               spectra[["Charge"]] %in% charges &
                               spectra[["Exposure"]] != 0]
    }
    spectra[["Exposure"]] <- paste0("Exposure: ", spectra[["Exposure"]])
    spectra[["Charge"]] <- paste0("Charge: ", spectra[["Charge"]])

    p <- ggplot(spectra, aes(x = Mz, xend = Mz, yend = Intensity, y = 0)) +
        geom_segment() +
        ylab("Intensity") +
        xlab("m/z") +
        theme_minimal() +
        theme(plot.title = element_text(hjust = 0.5), ...) +
        ggtitle(paste("Sequence:", unique(spectra[["Sequence"]]))) +
        facet_wrap(Charge~ Exposure, scales = "free")

    return(p)

}