#' @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

  )

}