diff --git a/R/findDE.R b/R/findDE.R index 1706d20..657ba4d 100644 --- a/R/findDE.R +++ b/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)")) } diff --git a/man/volcano_plot.Rd b/man/volcano_plot.Rd index d198d66..eeb6165 100644 --- a/man/volcano_plot.Rd +++ b/man/volcano_plot.Rd @@ -44,7 +44,7 @@ differential expression.} to indicate the \code{lfc} threshold in the plot.} \item{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.}} \item{palette}{Viridis color palette option for plots. Default is \code{"viridis"}. See @@ -82,8 +82,10 @@ This function generates volcano plots to visualize differentially expressed proteins between groups. } \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 +\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.}