R/plot_Volcano.R

In leandroroser/RNASeqFunctions: Several functions for rna-seq analysis

#' Volcano plots
#' @param x Output of edgeR::topTags
#' @param multiplot Draw multiple plots?
#' @param ncol Number of columns in grid
#' @param plot_title Titles for the plots
#' @export

plot_Volcano <- function(x, multiplot = FALSE,
                         plot_title, nrow, ncol) {

  single_plot <- function(data) {


    ggplot2::ggplot(data=data) +
      ggplot2::geom_point(aes(logFC, logP, col = de)) +
      ggplot2::xlab("logFC") +
      ggplot2::ylab("-log10(P-value)") +
      labs(color = "FDR")
  }


  if(multiplot) {
    merged_table <- list()

    for(i in seq_along(x)) {
       y <- x[[i]]$table
       merged_table[[i]] <- data.frame(logP = -log10(y$PValue),
                                      logFC = y$logFC,
                                      de = factor(c("NS", "FDR < 0.05")[as.numeric(y$FDR < 0.05) + 1]),
                                      contrast = rep(plot_title[i], nrow(y)))
    }

    merged_table <- do.call("rbind", merged_table)
    out <- single_plot(merged_table) +  ggplot2::facet_wrap(~contrast,
                                                      nrow = nrow,
                                                      ncol = ncol,
                                                      scales = c("free"))
    } else {
    out <- single_plot(x)
    if(!is.null(title)) {
      out <- out + ggtitle(plot_title)
    }
  }
  out
}