src/06_compute_tdd_index.R: add padj in TDD_correlation_table

src/06_compute_tdd_index.R

@@ -485,13 +485,18 @@ prepare_df_for_cor <- function(mean_gene_count = 10, ercc = F,
         clear = FALSE, # If TRUE, clears the bar when finish
         width = 100
     ) # Width of the progress bar
+    ptotv <- NULL
     for (gn in genes) {
         pb$tick()
         tmp <- tdd_full %>% filter(gene == gn)
         fit <- lm(value ~ condition + time_point + replicate, data = tmp)
         p_val <- summary(fit)$coefficients["conditionDMSO_TDD", "Pr(>|t|)"]
         tdd_mean[tdd_mean$gene == gn, "p_value"] <- p_val
+        ptotv <- c(ptotv, p_val)
     }
+    padjs <- p.adjust(ptotv, method = "fdr")
+    tmp_table <- tibble(gene = genes, padj = padjs)
+    tdd_mean <- tdd_mean %>% left_join(tmp_table, by = "gene")
     tdd_full <- tdd_mean %>% arrange(-p_value) # nolint
     write_tsv(tdd_full, paste0(output_folder, "/full_TDD_correlation_table.txt"))
     dir <- "./data/gene_lists/"
@@ -1064,6 +1069,7 @@ create_tdd_violin <- function(tp = 5, groupn = "up_down",
         )
         my_range <- c(-0.5, 1)
     } else {
+        tdd_table <- tdd_table %>% filter(group != "CTRL")
         title <- paste0(title, " for genes up and down by BRAFi")
         tdd_table$group <- factor(tdd_table$group,
             level = c("BRAF_UP", "BRAF_DOWN")