taxonomy_table function issue with add_id_column parameter.

[grabear]

taxa/R/taxonomy--class.R

Line 1079 in 2956cd6

taxonomy_table = function(subset = NULL, value = "taxon_names",

On multiple computers, I've had issues with the taxa::taxonomy_table function not adding the taxon_id column:

> taxonomy_table(metacoder_obj, subset = taxon_ids(metacoder_obj), add_id_col = TRUE)
# A tibble: 175 x 7
   Kingdom  Phylum          Class Order Family Genus Species
   <chr>    <chr>           <chr> <chr> <chr>  <chr> <chr>  
 1 Bacteria NA              NA    NA    NA     NA    NA     
 2 Bacteria Firmicutes      NA    NA    NA     NA    NA     
 3 Bacteria Proteobacteria  NA    NA    NA     NA    NA     
 4 Bacteria Spirochaetae    NA    NA    NA     NA    NA     
 5 Bacteria Verrucomicrobia NA    NA    NA     NA    NA     
 6 Bacteria Bacteroidetes   NA    NA    NA     NA    NA     
 7 Bacteria Fibrobacteres   NA    NA    NA     NA    NA     
 8 Bacteria Actinobacteria  NA    NA    NA     NA    NA     
 9 Bacteria Cyanobacteria   NA    NA    NA     NA    NA     
10 Bacteria Elusimicrobia   NA    NA    NA     NA    NA     
# ... with 165 more rows

However, when I use the function directly linked to the object it works without issue:

> metacoder_obj$taxonomy_table(subset = taxon_ids, add_id_col = TRUE)
# A tibble: 175 x 8
   taxon_id Kingdom  Phylum          Class Order Family Genus Species
 * <chr>    <fct>    <fct>           <fct> <fct> <fct>  <fct> <fct>  
 1 ac       Bacteria NA              NA    NA    NA     NA    NA     
 2 af       Bacteria Firmicutes      NA    NA    NA     NA    NA     
 3 ag       Bacteria Proteobacteria  NA    NA    NA     NA    NA     
 4 ah       Bacteria Spirochaetae    NA    NA    NA     NA    NA     
 5 ai       Bacteria Verrucomicrobia NA    NA    NA     NA    NA     
 6 aj       Bacteria Bacteroidetes   NA    NA    NA     NA    NA     
 7 ak       Bacteria Fibrobacteres   NA    NA    NA     NA    NA     
 8 al       Bacteria Actinobacteria  NA    NA    NA     NA    NA     
 9 an       Bacteria Cyanobacteria   NA    NA    NA     NA    NA     
10 ao       Bacteria Elusimicrobia   NA    NA    NA     NA    NA     
# ... with 165 more rows

[zachary-foster]

Hi @grabear, thanks for the report! I think i fixed it. Feel free to reopen this issue if it is not fixed.