Retrieve Taxonomic Lineage using taxonkit

Retrieve Taxonomic Lineage using taxonkit

taxonkit_lineage(
  file_path,
  delimiter = ";",
  no_lineage = FALSE,
  show_lineage_ranks = FALSE,
  show_lineage_taxids = FALSE,
  show_name = FALSE,
  show_rank = FALSE,
  show_status_code = FALSE,
  taxid_field = 1,
  text = FALSE,
  data_dir = NULL
)

Arguments

file_path

The path to the input file with taxonomic IDs. Or file text (text=TRUE)

delimiter

The field delimiter in the lineage (default ";").

no_lineage

Logical, indicating whether to exclude lineage information (default: FALSE).

show_lineage_ranks

Logical, indicating whether to append ranks of all levels in the lineage (default: FALSE).

show_lineage_taxids

Logical, indicating whether to append lineage consisting of taxids (default: FALSE).

show_name

Logical, indicating whether to append scientific name (default: FALSE).

show_rank

Logical, indicating whether to append rank of taxids (default: FALSE).

show_status_code

Logical, indicating whether to show status code before lineage (default: FALSE).

taxid_field

The field index of taxid. Input data should be tab-separated (default: 1).

text

logical,

data_dir

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

Value

A character vector containing the taxonomic lineage information.

See also

Other Rtaxonkit: check_taxonkit(), download_taxonkit_dataset(), install_taxonkit(), name_or_id2df(), taxonkit_filter(), taxonkit_lca(), taxonkit_list(), taxonkit_name2taxid(), taxonkit_reformat()

Examples

if (FALSE) { # \dontrun{
taxonkit_lineage("9606\n63221", show_name = TRUE, show_rank = TRUE, text = TRUE)
} # }