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nf-core · Nov 19, 2024 · 52f817e · 52f817e
1 parent 1a3bbc7
commit 52f817e
Showing 1 changed file with 21 additions and 22 deletions.
diff --git a/assets/differentialabundance_report.Rmd b/assets/differentialabundance_report.Rmd
@@ -896,28 +896,27 @@ for (i in 1:nrow(contrasts)){
             contrast_de <- round_dataframe_columns(contrast_de, digits=params$report_round_digits)
             print( htmltools::tagList(datatable(contrast_de, caption = paste('Differential genes', dir, 'in', contrast_descriptions[i], " (check", differential_files[[i]], "for more detail)"), rownames = FALSE) ))
 
-        # Check if Gene biotype column exists
-            if ("Gene biotype" %in% colnames(contrast_de)) {
-                # Plot Differentially Expressed Genes by Gene Biotype
-                gene_biotype_table <- contrast_de %>%
-                    group_by(`Gene biotype`) %>%
-                    summarise(count = dplyr::n(), .groups = 'drop') %>%
-                    filter(count > 0) %>%
-                    arrange(desc(count))
-
-                gene_biotype_plot <- ggplot(gene_biotype_table, aes(x = reorder(`Gene biotype`, -count), y = count)) +
-                    geom_bar(stat = "identity", position = position_dodge()) +
-                    labs(
-                        title = paste0("Differentially Expressed Genes by Gene Biotype (", dir, ")"),
-                        x = "Gene Biotype",
-                        y = "Number of Differentially Expressed Genes"  ) +
-                    theme_minimal() +
-                    theme(axis.text.x = element_text(angle = 45, hjust = 1))
-
-                print(gene_biotype_plot)
-                } else {
-                    cat("Column 'Gene biotype' does not exist. Skipping plot.\n")
-                }
+        if ("Gene biotype" %in% colnames(contrast_de)) {
+        # Plot Differentially Expressed Genes by Gene Biotype
+        gene_biotype_table <- contrast_de %>%
+            group_by(`Gene biotype`) %>%
+            summarise(count = dplyr::n(), .groups = 'drop') %>%
+            filter(count > 0) %>%
+            arrange(desc(count))
+
+        gene_biotype_plot <- ggplot(gene_biotype_table, aes(x = reorder(`Gene biotype`, -count), y = count)) +
+            geom_bar(stat = "identity", position = position_dodge()) +
+            labs(
+                title = paste0("Differentially Expressed Genes by Gene Biotype (", dir, ")"),
+                x = "Gene Biotype",
+                y = "Number of Differentially Expressed Genes"  ) +
+            theme_minimal() +
+            theme(axis.text.x = element_text(angle = 45, hjust = 1))
+
+        print(gene_biotype_plot)
+        } else {
+            cat("Column 'Gene biotype' does not exist. Skipping plot.\n")
+        }
         }else{
             cat(paste0("No significantly differential '", dir, "' genes.\n\n"))
         }