R/differiential_expression.R: update dot dot notation with after_stat

R/differiential_expression.R

@@ -66,7 +66,7 @@ create_de_figures <- function(df, output_folder, condition, lfct) {
         }
     }
     pp <- ggplot(data = dfn, mapping = aes(
-        x = padj, y = (..count..) / sum(..count..)
+        x = padj, y = (after_stat(count)) / sum(after_stat(count))
     )) +
         geom_histogram() +
         labs(y = "Proportion of corrected p-values", x = "P-value corrected") +
@@ -171,7 +171,7 @@ create_de_figures <- function(df, output_folder, condition, lfct) {
 #' @param output_folder Folder where the result table will be created
 #' @param basemean_threshold: The minimum basemean of gene to be knameept
 #' @param lfc_threshold The minimum fold change to consider a gene significant
-#' @param gene_names A dataframe with the columns gene_id and gene_name, 
+#' @param gene_names A dataframe with the columns gene_id and gene_name,
 #' (default NULL).
 #' @return A list containing:
 #' 1. at `data` key: A dataframe indicating The number of differentially
@@ -252,7 +252,7 @@ de_analysis <- function(dds, my_contrast, output_folder, basemean_threshold,
 #' @param output_folder Folder where the result table will be created
 #' @param basemean_threshold: The minimum basemean of genes to be kept
 #' @param lfc_threshold The minimum fold change to consider a gene significant
-#' @param gene_names A dataframe with the columns gene_id and gene_name, 
+#' @param gene_names A dataframe with the columns gene_id and gene_name,
 #' (default NULL).
 #'
 #' @return A list containing for each comparison given in my_contrasts