Functions for importing output of `sourmash taxonomy annotate` into metacoder object

[taylorreiter]

• metacoder visualization
  • read_sourmash_taxonomy_annotate(file, intersect_bp_threshold)
  • pivot_sourmash_taxonomy_annotate_wider()
  • sourmash_taxonomy_annotate_to_metacoder(sourmash_taxonomy_annotate_df, database = c("genbank", "gtdb"), summary_level = c(NULL, "genus", ...))
    • database will control class_regex for parse_tax_data()
    • summary_level will control if the sourmash results are agglomerated up the taxonomic lineage during the creation of the metacoder object (e.g. to genus level).
    • sequence of functions:
      • read_sourmash_taxonomy_annotate() to purrr::map_dfr
      • pivot_sourmash_taxonomy_annotate_wider()
      • parse_tax_data()
      • calc_taxon_abund()
      • calc_n_samples()
    • goal is to do everything that a user would need to think of doing to get the data into metacoder land to enable visualization. Check and see if there is something that needs to be done for diff abund vix/matrix viz.

[taylorreiter]

Closed by #8