R/rawpHist.R

In PF2-pasteur-fr/SARTools: Statistical Analysis of RNA-Seq Tools

#' Histograms of raw p-values
#'
#' Histogram of raw p-values for each comparison
#'
#' @param complete a list of \code{data.frames} created by \code{summaryResults.DESeq2()} or \code{summaryResults.edgeR()}
#' @param outfile TRUE to export the figure in a png file
#' @param ggplot_theme ggplot2 theme function (\code{theme_gray()} by default)
#' @return A file named rawpHist.png in the figures directory with one histogram of raw p-values per comparison
#' @author Marie-Agnes Dillies and Hugo Varet

rawpHist <- function(complete, outfile=TRUE, ggplot_theme=theme_gray()){
  ncol <- min(2, length(complete))
  nrow <- ceiling(length(complete)/ncol)
  if (outfile) png(filename="figures/rawpHist.png", width=cairoSizeWrapper(1800*ncol), height=cairoSizeWrapper(1800*nrow), res=300)
  p <- list()
  for (name in names(complete)){
    complete.name <- complete[[name]]
    complete.name <- complete.name[which(!is.na(complete.name$pvalue)),]
    p[[name]] <- ggplot(data=complete.name, aes(x=.data$pvalue)) +
      geom_histogram(color="white", breaks=seq(0, 1, by=0.025)) +
      scale_y_continuous(expand=expansion(mult=c(0.01, 0.05))) +
      xlab("Raw p-value") +
      ylab("Frequency") +
      ggtitle(paste0("Distribution of raw p-values - ", gsub("_"," ",name))) +
      ggplot_theme
  }
  tmpfun <- function(...) grid.arrange(..., nrow=nrow, ncol=ncol)
  do.call(tmpfun, p)
  if (outfile) dev.off()
}