R/barplot_pwys.R

In jdreyf/ezlimmaplot: Bioinformatics plots using limma and ggplot2, some from output of ezlimma

#' Make barplots for the p-Values of Pathway Analysis
#'
#' Make barplots for the p-Values of pathway analysis using \pkg{ggplot2}.
#'
#' @param ntop Number of top pathways.
#' @param direction Direction of change.
#' @param pwys_nm_size The maximum number of characters for pathway names. Longer names will be truncated.
#' @inheritParams ezheat
#' @inheritParams ezvenn
#' @return Invisibly, the last ggplot object.
#' @export
#'

barplot_pwys <- function(tab, prefix.v=NULL, name = NA, width = 10, height = 4, ntop = 20, direction = c("Up", "Down"), pwys_nm_size = 100){
  if (is.null(prefix.v)){
    p.colnms <- ezlimma:::grep_cols(tab=tab, p.cols="p")
    p.colnms <- p.colnms[-grep("Mixed", p.colnms)]
    prefix.v <- gsub(pattern = "(\\.|^)p$", replacement = "", x=p.colnms)
    stopifnot(sapply(tab[, grep("Direction$", colnames(tab)), drop=FALSE], FUN=function(vv) all(direction %in% vv )))
  } else {
    stopifnot(sapply(tab[, paste0(prefix.v, ".Direction"), drop=FALSE], FUN=function(vv) all(direction %in% vv )))
  }

  if (!is.na(name)){
    name <- paste0(name, "_barplots.pdf")
    grDevices::pdf(name, width, height)
    on.exit(grDevices::dev.off())
  }

  for (prefix in prefix.v){
    tab.sub <- tab[, c("NGenes", paste(prefix, c("Direction", "p"), sep = ".")), drop=FALSE]
    colnames(tab.sub) <- gsub(paste0(prefix, "."), "", colnames(tab.sub))
    tab.sub <- tab.sub[order(tab.sub$p), ]

    for(d in direction) {
      dat2p <- tab.sub[tab.sub$Direction == d,, drop=FALSE]
      dat2p <- dat2p[1:min(ntop, nrow(dat2p)),, drop=FALSE]
      dat2p$Pathway <- substr(rownames(dat2p), 1, pwys_nm_size)
      dat2p$Pathway <- gsub("_", " ", dat2p$Pathway)
      dat2p$Pathway <- factor(dat2p$Pathway, levels = rev(dat2p$Pathway))
      dat2p$NGenes <- paste0("(", dat2p$NGenes, ")")
      dat2p$neglog10p <- - log10(dat2p$p)

      ggp <- ggplot2::ggplot(dat2p, mapping=ggplot2::aes(Pathway, neglog10p)) + ggplot2::theme_bw() + ggplot2::coord_flip()
      ggp <- ggp + ggplot2::labs(x = "", y = expression("-"*log[10]~p*"-"*value), title = paste0(prefix, ", ", d, "-regulated"))

      if (d == "Up") {
        ggp <- ggp + ggplot2::geom_bar(stat = "identity", width = 0.7, fill = "red")
        ggp <- ggp + ggplot2::geom_text(ggplot2::aes(label = NGenes), hjust = -0.1) + ggplot2::ylim(0, 1.05*dat2p$neglog10p[1])
      } else {
        ggp <- ggp + ggplot2::geom_bar(stat = "identity", width = 0.7, fill = "blue") +
          ggplot2::scale_y_reverse(limits=c(1.05*dat2p$neglog10p[1], 0)) +
          ggplot2::geom_text(ggplot2::aes(label = NGenes), hjust = 1.1)
      }
      graphics::plot(ggp)
    } #end for d
  }
  invisible(ggp)
}