--- a
+++ b/R/VolcanoPlot.R
@@ -0,0 +1,77 @@
+#' @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
+  )
+}