From b7df1e0be62d9e445bc8a0e80aadbfa412ce559d Mon Sep 17 00:00:00 2001
From: gmteunisse <gmteunisse@gmail.com>
Date: Mon, 26 Sep 2022 11:49:38 +0200
Subject: [PATCH] Changed default asv_as_id = T. Made sure that when tax_level
 is defined, no duplicates occur. Workaround for issue #10.

---
 R/label_duplicate_taxa.R    | 28 ++++++++++++++++++----------
 man/label_duplicate_taxa.Rd |  2 +-
 2 files changed, 19 insertions(+), 11 deletions(-)

diff --git a/R/label_duplicate_taxa.R b/R/label_duplicate_taxa.R
index 56db52e..48d1c5f 100644
--- a/R/label_duplicate_taxa.R
+++ b/R/label_duplicate_taxa.R
@@ -33,7 +33,7 @@
 #' ps_tmp <- label_duplicate_taxa(GlobalPatterns, tax_level = "Species")
 #' View(tax_table(ps_tmp))
 #' @export
-label_duplicate_taxa <- function(ps_obj, tax_level = NULL, asv_as_id = F,
+label_duplicate_taxa <- function(ps_obj, tax_level = NULL, asv_as_id = T,
                                  duplicate_label = "<tax> <id>"){
 
   # Check arguments
@@ -47,15 +47,18 @@ label_duplicate_taxa <- function(ps_obj, tax_level = NULL, asv_as_id = F,
 
   # Find duplicate taxa and flag for labeling
   tax_tab <- tax_table(ps_obj) %>%
-    data.frame(row_name = row.names(.)) %>%
-    group_by(across(-row_name)) %>%
-    mutate(n = row_number(),
-           dupl = n > 1) %>%
-    mutate(add_label = sum(dupl) > 0)
+    data.frame(row_name = row.names(.))
 
   # Add label to the lowest non-NA taxonomic level
   if(is.null(tax_level)){
 
+    # Find duplicates
+    tax_tab <- tax_tab %>%
+      group_by(across(-row_name)) %>%
+      mutate(n = row_number(),
+             dupl = n > 1) %>%
+      mutate(add_label = sum(dupl) > 0)
+
     # Convert to long
     tax_tab <- tax_tab %>%
       pivot_longer(!c(row_name, n, dupl, add_label),
@@ -71,7 +74,7 @@ label_duplicate_taxa <- function(ps_obj, tax_level = NULL, asv_as_id = F,
                             tax),
              tax = str_replace(label, "<tax>", tax))
 
-    # Fill in id field
+    # Fill in id field with either the row number or the ASV ID (row_name)
     if(asv_as_id){
       tax_tab <- tax_tab %>%
         mutate(tax = str_replace(tax, "<id>", as.character(row_name)))
@@ -86,9 +89,16 @@ label_duplicate_taxa <- function(ps_obj, tax_level = NULL, asv_as_id = F,
       select(!c(n, dupl, add_label, label)) %>%
       pivot_wider(names_from = rank, values_from = tax)
 
-  # Add a label to a specific taxonomic rank
+    # Add a label to a specific taxonomic rank
   } else {
 
+    # Find duplicates
+    tax_tab <- tax_tab %>%
+      group_by(!!sym(tax_level)) %>%
+      mutate(n = row_number(),
+             dupl = n > 1) %>%
+      mutate(add_label = sum(dupl) > 0)
+
     # Add label and fill in tax field
     tax_tab <- tax_tab %>%
       mutate(label = ifelse(add_label,
@@ -119,6 +129,4 @@ label_duplicate_taxa <- function(ps_obj, tax_level = NULL, asv_as_id = F,
   return(ps_obj)
 
 
-
-
 }
diff --git a/man/label_duplicate_taxa.Rd b/man/label_duplicate_taxa.Rd
index a511430..0461afa 100644
--- a/man/label_duplicate_taxa.Rd
+++ b/man/label_duplicate_taxa.Rd
@@ -7,7 +7,7 @@
 label_duplicate_taxa(
   ps_obj,
   tax_level = NULL,
-  asv_as_id = F,
+  asv_as_id = T,
   duplicate_label = "<tax> <id>"
 )
 }