R/VolcanoPlot.R

In DIscBIO: A User-Friendly Pipeline for Biomarker Discovery in Single-Cell Transcriptomics

#' @title Volcano Plot
#' @description Plotting differentially expressed genes (DEGs) in a particular
#'   cluster. Volcano plots are used to readily show the DEGs by plotting
#'   significance versus fold-change on the y and x axes, respectively.
#' @param object A data frame showing the differentially expressed genes (DEGs)
#'   in a particular cluster
#' @param value A numeric value of the false discovery rate. Default is 0.05..
#'   Default is 0.05
#' @param fc A numeric value of the fold change. Default is 0.5.
#' @param FS A numeric value of the font size. Default is 0.4.
#' @param name A string vector showing the name to be used on the plot title
#' @importFrom graphics title
#' @importFrom utils write.csv
#' @return A volcano plot
#' @export
VolcanoPlot <- function(object, value = 0.05, name = NULL, fc = 0.5, FS = .4) {
  if (length(object[1, ]) > 8) {
    object <- object[, -1]
  }
  NO0 <- object[, 8]
  NO0 <- NO0[which(NO0 != 0)]
  w <- which.min(NO0)
  adjV <- NO0[w] / 100
  object[, 8] <- ifelse(
    object[, 8] == 0 & length(adjV) > 0, adjV, object[, 8]
  )
  if (all(object[, 8] == 0)) {
    message("All q-values are 0. Adjusting")
    object[, 8] <- object[, 8] + 1e-10
  }
  with(
    object,
    plot(
      abs(object[, 7]),
      -log10(object[, 8]),
      pch = 20,
      cex = 2,
      las = 1,
      xlab = "log2 Fold Change",
      ylab = "-log10 FDR",
      sub = paste("Volcano plot", name),
      font.sub = 4,
      col.sub = "black"
    )
  )
  FC <- subset(object, abs(object[, 7]) > fc) # Fold Change
  sigFC <- subset(
    object, object[, 8] < value & abs(object[, 7]) > fc
  ) # Significant genes
  with(FC, points(
    abs(FC[, 7]),
    -log10(FC[, 8]),
    pch = 20,
    cex = 2,
    col = "red"
  ))
  with(sigFC, points(
    abs(sigFC[, 7]),
    -log10(sigFC[, 8]),
    pch = 20,
    cex = 2,
    col = "blue"
  ))
  add_legend(
    "topleft",
    legend = c(
      paste0("DEGs (FC < ", fc, " - FDR> ", value, ")   "),
      paste0("DEGs (FC > ", fc, " - FDR> ", value, ")"),
      paste0("DEGs (FC > ", fc, " - FDR< ", value, ")   ")
    ),
    pch = 20,
    col = c("black", "red", "blue"),
    horiz = TRUE,
    bty = "n",
    cex = FS
  )
}