Summarize taxonomy quality with external file support — summarize_taxonomy_quality_with

Extended version of summarize_taxonomy_quality() that can use an external taxonomy file.

Usage

summarize_taxonomy_quality_with_file(
  labels,
  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.
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. 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). Default: NULL.

Value

Invisibly returns a list with parsing statistics.