Testing new preserve argument in tax_agg

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: microViz
 Title: Microbiome Data Analysis and Visualization
-Version: 0.10.0
+Version: 0.10.0.9000
 Authors@R: 
     person(given = "David",
            family = "Barnett",

NEWS.md

@@ -1,3 +1,5 @@
+# microViz (development version)
+
 # microViz 0.10.0
 
 Major internal changes from S3 ps_extra to S4 psExtra objects. See [article about this change](../articles/ps_extra-replaced.html)

R/tax_agg.R

@@ -102,6 +102,7 @@ tax_agg <- function(ps,
                     sort_by = NA,
                     top_N = NA,
                     force = FALSE,
+                    preserve = NULL,
                     add_unique = FALSE) {
   stopif_ps_extra(ps, argName = "ps")
   check_is_phyloseq(ps, argName = "ps")
@@ -150,6 +151,18 @@ tax_agg <- function(ps,
       stop("zero-length name(s) in tax_table at rank: ", rank, taxFixPrompt())
     }
 
+    # copy taxa names to aggregation rank if some taxa marked as preserved
+    if (!is.null(preserve)) {
+      preserve <- rlang::arg_match(
+        arg = preserve, values = uniqueNamesAtRank, multiple = TRUE
+      )
+      preserved <- tt_df[[rank_index]] %in% preserve
+      tt_df[preserved, rank_index] <- rownames(tt_df)[preserved]
+      uniqueNamesAtRank <- unique(tt_df[, rank_index])
+      # change name of rank to indicate it's not a pure rank aggregation
+      rank <- names(tt_df)[names(tt_df) == rank] <- paste(rank, "& unique")
+    }
+
     if (isTRUE(force)) {
       # FORCED aggregation: doesn't care/check if higher ranks are not unique
       tt_distinct <- dplyr::distinct(