Revert back to original names when exporting

R/app_server.R

@@ -85,7 +85,11 @@ app_server <- function(input, output, session) {
       content = function(con) {
         ## Update taxonomy of object phyloseq
         phyloseq::tax_table(physeq)[rownames(affiliations$cleaned), ] <- affiliations$cleaned
-        ## TODO revert short OTU names back to original names
+        ## revert short OTU names back to original names
+        dict <- setNames(object = otu_dictionary$sequence, 
+                         nm     = otu_dictionary$OTU)
+        phyloseq::taxa_names(physeq) <- dict[phyloseq::taxa_names(physeq)]
+        ## Export 
         phyloseq.extended::write_phyloseq(
           physeq = physeq, 
           biom_file = con, 

R/utils.R

@@ -26,7 +26,7 @@ create_otu_dictionary <- function(physeq) {
     abundance = phyloseq::taxa_sums(physeq)
   ) %>% 
     dplyr::arrange(desc(abundance))
-  ## If all taxa names are long, sequences are likely to have been processed by DADA
+  ## If all taxa names are long, sequences are likely to have been processed by DADA2
   ## Move OTU names to sequence column and rename OTU with shorter names
   if (long_taxa_names(otu_dictionary$sequence)) {
    otu_dictionary <- otu_dictionary %>%