fix file naming, show only sig pathways

bcbio · Nov 4, 2024 · c88bcae · c88bcae
1 parent 96e19c6
commit c88bcae
Showing 1 changed file with 8 additions and 8 deletions.
diff --git a/inst/templates/rnaseq/DE/DEG.Rmd b/inst/templates/rnaseq/DE/DEG.Rmd
@@ -570,7 +570,7 @@ fa_gsea_list=lapply(de_list,function(contrast){
 # multiple times
 dt_list=list()
 for (contrast in names(de_list)){
-  res_sig=fa_gsea_list[[contrast]]
+  res_sig=fa_gsea_list[[contrast]] %>% filter(padj < 0.05)
   dt_list=c(dt_list, 
             list(h3(contrast)), 
             list(sanitize_datatable(res_sig)))
@@ -621,7 +621,7 @@ fa_list=lapply(de_list,function(contrast){
 # multiple times
 dt_list=list()
 for (contrast in names(de_list)){
-  res_sig=fa_list[[contrast]][["all"]]
+  res_sig=fa_list[[contrast]][["all"]] %>% filter(padj < 0.05)
   dt_list=c(dt_list, 
             list(h3(contrast)), 
             list(sanitize_datatable(res_sig)))
@@ -635,7 +635,7 @@ tagList(dt_list)
 ```{r, results='asis'}
 dt_list=list()
 for (contrast in names(de_list)){
-  res_sig=fa_list[[contrast]][["down"]]
+  res_sig=fa_list[[contrast]][["down"]] %>% filter(padj < 0.05)
   dt_list=c(dt_list, 
             list(h3(contrast)), 
             list(sanitize_datatable(res_sig)))
@@ -649,7 +649,7 @@ tagList(dt_list)
 ```{r, results='asis'}
 dt_list=list()
 for (contrast in names(de_list)){
-  res_sig=fa_list[[contrast]][["up"]]
+  res_sig=fa_list[[contrast]][["up"]] %>% filter(padj < 0.05)
   dt_list=c(dt_list, 
             list(h3(contrast)), 
             list(sanitize_datatable(res_sig)))
@@ -667,18 +667,18 @@ if (!is.null(subset_value) & !is.null(subset_value)){
   filenames = "full"
 }
 for (contrast in names(contrasts)){
-  filenames = paste0(filenames, "_", contrast)
+  filename = paste0(filenames, "_", contrast)
   name_expression_fn=file.path(
     basedir,
-    str_interp("${filenames}_expression.csv"))
+    str_interp("${filename}_expression.csv"))
   
   name_deg_fn=file.path(
     basedir,
-    str_interp("${filenames}_deg.csv"))
+    str_interp("${filename}_deg.csv"))
   
   name_pathways_fn=file.path(
     basedir,
-    str_interp("${filenames}_pathways.csv"))
+    str_interp("${filename}_pathways.csv"))
 
   counts_norm=norm_matrix %>% as.data.frame() %>% 
     rownames_to_column("gene_id") %>%