R/ms_plot.R

In TalhoukLab/biostatUtil: Utility Functions Used in Biostatistics Projects

#' Plots for MS analyses
#'
#' `ms_boxplot` shows boxplots of different MS expression data values.
#' `ms_mean_var` shows mean-sd plots for the VSN data values to analyze the
#' mean-variance relationship.
#'
#' @param x data object returned by `ms_process`
#' @param width width of plot
#' @param height height of plot
#' @param path file path to save figure. Device is pdf.
#' @return Both functions return a pdf saved to the file location specified by
#'   `path`. `ms_boxplot` shows three boxplots of expression values:
#'   raw data values, log2 and vsn transformed values. `ms_mean_var` shows
#'   the vsn transformed values and mean-sd plots for each treatment group.
#' @name ms_plot
#' @family Mass Spectrometry functions
#' @author Derek Chiu
#' @export
ms_boxplot <- function(x, width = 8, height = 10, path = NULL) {
  dat.plot <- lapply(x[c("raw", "l2", "vsn")], function(y)
    tidyr::gather(as.data.frame(y), key = "Sample", value = "Expression"))
  all.plots <- Map(ms_gg_boxplot, dat.plot,
                   c("Raw data values",
                     "log2(Raw data values)",
                     "vsn(Raw data values)"))
  plot <- gridExtra::marrangeGrob(all.plots, nrow = 1, ncol = 1, top = NULL)
  if (!is.null(path))
    ggsave(filename = path, plot = plot, width = width, height = height)
  return(all.plots)
}

#' ggplot boxplot applied to each data source
#' @noRd
ms_gg_boxplot <- function(x, title) {
  p <- ggplot(x, aes(x = .data$Sample, y = .data$Expression)) +
    stat_boxplot(geom = "errorbar", width = 0.4) +
    geom_boxplot() +
    theme_linedraw() +
    theme(plot.title = element_text(face = "bold"),
          panel.grid = element_blank(),
          axis.text.x = element_text(angle = 45, vjust = 1, hjust = 1)) +
    ggtitle(title)
  return(p)
}

#' @param g vector of treatment groups
#' @param title vector of titles for each `g`
#' @name ms_plot
#' @export
ms_mean_var <- function(x, g, title = NULL, width = 8, height = 10,
                        path = NULL) {
  if (is.null(title)) title <- g
  dat.plot <- tidyr::gather(as.data.frame(x[["vsn"]]),
                            key = "Sample", value = "Expression")
  bp <- ms_gg_boxplot(dat.plot, "vsn(Raw data values)")
  msdp <- Map(function(g, t)
    vsn::meanSdPlot(x$vsn[, grep(g, colnames(x$vsn))], plot = FALSE)$gg +
      ggtitle(paste("vsn", t)), g = g, t = title)
  all.plots <- append(list(bp), unname(msdp))
  plot <- gridExtra::marrangeGrob(all.plots, nrow = 1, ncol = 1, top = NULL)
  if (!is.null(path))
    ggsave(filename = path, plot = plot, width = width, height = height)
  return(all.plots)
}