Verified Commit c183a845 authored by nfontrod's avatar nfontrod
Browse files

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

parent aba6bfc2
......@@ -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
......
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