taxonomy_table function issue with add_id_column parameter. #191
Description
Line 1079 in 2956cd6
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 rowsHowever, 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