volcano_plot function updated to show adj.Pval on y-axis

R/findDE.R

@@ -191,7 +191,7 @@ find_dep <- function(df,
 #' @param line_fc Logical. If \code{TRUE}(default), a dotted line will be shown
 #' to indicate the \code{lfc} threshold in the plot.
 #' @param line_p Logical. If \code{TRUE}(default), a dotted line will be shown
-#' to indicate the p-value \code{cutoff.}
+#' to indicate the p-value or adjusted p-value \code{cutoff.}
 #' @param palette Viridis color palette option for plots. Default is
 #' \code{"viridis"}. See
 #' \code{\link[viridis:viridis]{viridis}}
@@ -212,8 +212,10 @@ find_dep <- function(df,
 #' \code{label_top = TRUE.} Default is \code{10}.
 #' @param dpi Plot resolution. Default is \code{80.}
 #'
-#' @details \itemize{\item Volcano plots show log-2-fold change on the x-axis
-#' and -log10(p-value) on the y-axis.\item \code{volcano_plot} requires a
+#' @details \itemize{\item Volcano plots show log-2-fold change on the x-axis,
+#' and based on the significance criteria chosen, either -log10(p-value) or
+#' -log10(adjusted p-value) on the y-axis.
+#' \item \code{volcano_plot} requires a
 #' \code{fit_df} object from performing differential expression analysis
 #' with \code{find_dep.}
 #' \item User has the option to choose criteria that denote significance.}
@@ -288,21 +290,24 @@ volcano_plot <- function(fit_df,
  ggplot2::geom_point(aes(color = dep),
  alpha = 0.7,
  size = text_size * 0.3
- )
+ )+
+ ggplot2::ylab(expression("-log"[10] * "(P-value)"))
+
  } else {
  res_de <- res_de[order(-res_de$de_ap, res_de$adj.P.Val), ]
  de_volcanoplot <- ggplot2::ggplot(
  res_de,
  aes(
  x = logFC,
- y = -log10(P.Value),
+ y = -log10(adj.P.Val),
  color = de_ap
  )
  ) +
  ggplot2::geom_point(aes(color = de_ap),
  alpha = 0.7,
  size = text_size * 0.3
- )
+ )+
+ ggplot2::ylab(expression("-log"[10] * "(adj.P-value)"))
  }