Fixed GSEA section indent in report

nf-core · Nov 8, 2023 · aaed90f · aaed90f
1 parent 2f65398
commit aaed90f
Showing 1 changed file with 5 additions and 9 deletions.
diff --git a/assets/differentialabundance_report.Rmd b/assets/differentialabundance_report.Rmd
@@ -793,21 +793,17 @@ if (any(unlist(params[paste0(possible_gene_set_methods, '_run')]))){
 
   for (gene_set_method in possible_gene_set_methods){
     if (unlist(params[paste0(gene_set_method, '_run')])){
-      cat("\n### ", toupper(gene_set_method) ," {.tabset}\n")
+      cat("\n#### ", toupper(gene_set_method) ," {.tabset}\n")
       
       for (gmt_file in simpleSplit(params$gsea_gene_sets)) {
         gmt_name <- basename(tools::file_path_sans_ext(gmt_file))
-
-        cat("\n#### ", gmt_name ," {.tabset}\n")
+        cat("\n##### ", gmt_name ," {.tabset}\n")
         reference_gsea_tables <- paste0(contrasts$id, ".", gmt_name, '.gsea_report_for_', contrasts$reference, '.tsv')
         target_gsea_tables <- paste0(contrasts$id, ".", gmt_name, '.gsea_report_for_', contrasts$target, '.tsv')
-
         for (i in 1:nrow(contrasts)){
-          cat("\n##### ", contrast_descriptions[i], "\n")
-
+          cat("\n###### ", contrast_descriptions[i], "\n")
           target_gsea_results <- read_metadata(target_gsea_tables[i])[,c(-2,-3)]
           print( htmltools::tagList(datatable(target_gsea_results, caption = paste0("\nTarget (", contrasts$target[i], ")\n"), rownames = FALSE) ))
-
           ref_gsea_results <- read_metadata(reference_gsea_tables[i])[,c(-2,-3)]
           print( htmltools::tagList(datatable(ref_gsea_results, caption = paste0("\nReference (", contrasts$reference[i], ")\n"), rownames = FALSE) ))
         }
@@ -874,7 +870,7 @@ if (any(unlist(params[paste0(possible_gene_set_methods, '_run')]))){
 
   for (gene_set_method in possible_gene_set_methods){
     if (unlist(params[paste0(gene_set_method, '_run')])){
-      cat("\n### ", toupper(gene_set_method) ,"  {.tabset}\n")
+      cat("\n#### ", toupper(gene_set_method) ,"  {.tabset}\n")
       make_params_table(toupper(gene_set_method), paste0(gene_set_method, '_'), remove_pattern = TRUE)
     }
   }
@@ -902,4 +898,4 @@ print( htmltools::tagList(datatable(versions_table, caption = "Software versions
 
 ```{r, echo=FALSE, results='asis'}
 htmltools::includeMarkdown(params$citations)
-```
+```