Transfer taxon name or taxid to the lineage dataframe

Transfer taxon name or taxid to the lineage dataframe

name_or_id2df(
  name_or_id,
  mode = "name",
  add_prefix = TRUE,
  fill_miss_rank = TRUE,
  data_dir = NULL,
  format_string = "",
  use_taxonkit_reformat2 = FALSE,
  ...
)

Arguments

name_or_id

name or taxid

mode

"id" or "name"

add_prefix

add_prefix

fill_miss_rank

fill_miss_rank

data_dir

directory containing nodes.dmp and names.dmp (default "/Users/asa/.taxonkit")

format_string

The output format string with placeholders for each rank. Try "d;p;c;o;f;g;s" if you use NCBI taxonomy database later than 2025-04.

use_taxonkit_reformat2

use taxonkit_reformat2 rather than taxonkit_reformat, if you use NCBI taxonomy database later than 2025-04.

...

parameters pass to taxonkit_reformat or taxonkit_reformat2

Value

dataframe

See also

Other Rtaxonkit: check_taxonkit(), download_taxonkit_dataset(), install_taxonkit(), taxonkit_filter(), taxonkit_lca(), taxonkit_lineage(), taxonkit_list(), taxonkit_name2taxid(), taxonkit_reformat(), taxonkit_reformat2()

Examples

if (FALSE) { # \dontrun{
name_or_id2df(c("Homo sapiens", "Akkermansia muciniphila ATCC BAA-835"))
name_or_id2df(c("Homo sapiens", "Akkermansia muciniphila ATCC BAA-835"),
  format_string = "{d};{p};{c};{o};{f};{g};{s}"
)
name_or_id2df(c("Homo sapiens", "Akkermansia muciniphila ATCC BAA-835"),
  use_taxonkit_reformat2 = TRUE
)
} # }