parse_taxonomy_with_file: Parse taxonomy with external file support
In Rclade: Automated Deep-Time Phylogenetic Tree Collapsing and Visualization

parse_taxonomy_with_file

R Documentation

Parse taxonomy with external file support

Description

Extended taxonomy parsing that can use an external taxonomy file to supplement or override label-based parsing. Useful when:

Tip labels lack taxonomy information
Only some tips have taxonomy in their labels
External taxonomy data is more complete or accurate

Usage

parse_taxonomy_with_file(
  labels,
  rank,
  format = "auto",
  custom_patterns = NULL,
  taxonomy_file = NULL,
  file_sep = "auto",
  file_header = FALSE,
  file_priority = TRUE,
  table_sep = ";",
  delimiter_mode = "reverse",
  taxonomy_levels = NULL
)

Arguments

`labels`	Character vector of tip labels.
`rank`	Taxonomic rank (abbreviation or full name).
`format`	Format: "auto", "GTDB", "Silva", "NCBI", "custom_rank", "custom_regex".
`custom_patterns`	Custom regex patterns (for "custom_regex" format).
`taxonomy_file`	Character. Path to external taxonomy file. Default: `NULL`.
`file_sep`	Character. Column separator for taxonomy file. Default: `"auto"`.
`file_header`	Logical. Whether taxonomy file has header row. Default: `FALSE`.
`file_priority`	Logical. If `TRUE`, file taxonomy takes priority over label-based parsing. If `FALSE`, file is used only for labels that cannot be parsed from the tree. Default: `TRUE`.
`table_sep`	Character. Separator between taxonomy ranks in the second column of the taxonomy file. Default: `";"`.
`delimiter_mode`	Character. Embedded parsing strategy: "reverse", "greedy", "segment".
`taxonomy_levels`	Custom taxonomy level configuration (list with codes and names). Used to extend or override default rank handling. Default: `NULL`.