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Get biotic interactions for taxa present in a phyloseq object using rglobi

Source: R/tax_globi_pq.R
tax_globi_pq.Rd

A wrapper of [rglobi::get_interactions_by_taxa()] function to get biotic interactions for each taxa of a phyloseq object

Usage

tax_globi_pq(
  physeq = NULL,
  taxnames = NULL,
  taxonomic_rank = "currentCanonicalSimple",
  discard_synonym = TRUE,
  add_to_phyloseq = NULL,
  col_prefix = NULL,
  interaction_types = NULL,
  valid_taxo_target_taxon = TRUE,
  add_target_canonical = TRUE,
  data_sources = c(1, 12),
  verbose = FALSE,
  strict_interaction_types = TRUE,
  max_interactions = 1000,
  batch_size_gna_verifier = 50,
  discard_genus_alone = taxonomic_rank == "currentCanonicalSimple",
  discard_NA = TRUE
)

Arguments

physeq

(optional) A phyloseq object. Either `physeq` or `taxnames` must be provided, but not both.

taxnames

(optional) A character vector of taxonomic names.

taxonomic_rank

(Character, default "currentCanonicalSimple") The column(s) present in the @tax_table slot of the phyloseq object. Can be a vector of two columns (e.g. c("Genus", "Species")).

discard_synonym

(logical, default TRUE) If TRUE, discard interactions where the source_taxon_name is a synonym of the taxon name used to query

add_to_phyloseq

(logical, default TRUE when physeq is provided, FALSE when taxnames is provided) If TRUE, return a new phyloseq object with new columns in the tax_table slot. If FALSE, return a tibble with the interactions found for each taxon. Automatically set to TRUE when a phyloseq object is provided and FALSE when taxnames is provided. Cannot be TRUE if `taxnames` is provided.

col_prefix

A character string to be added as a prefix to the new columns names added to the tax_table slot of the phyloseq object (default: NULL).

interaction_types

A character vector of interaction types to query. See [rglobi::get_interaction_types()]. If NULL (default), all interaction types are queried.

valid_taxo_target_taxon

(logical, default TRUE) If TRUE, verify the scientific names of the target_taxon_name using [taxize::gna_verifier()] function and keep only valid names.

add_target_canonical

(logical, default TRUE) If TRUE, add a column `target_taxon_Canonical` with the current accepted name (resolve the synonymie) of the target_taxon_name using [taxize::gna_verifier()] function.

data_sources

A character or integer vector with numbers corresponding to data sources. See the Global Names Architecture documentation for a list of available options.

verbose

(logical, default FALSE) If TRUE, prompt some messages.

strict_interaction_types

(logical, default TRUE) If TRUE, keep only interactions exactly matching the interaction_types provided. If FALSE, keep all interactions returned by rglobi for the queried taxon. For exemple, rglobi for interaction_types = "hasHost" will also return interactions with interaction_type = "pathogenOf" and "parasiteOf" if strict_interaction_types is set to FALSE.

max_interactions

(numeric, default 1000) The maximum number of interactions to query for each taxon.

batch_size_gna_verifier

(numeric, default 100) The number of names to verify at once with' [taxize::gna_verifier()] function. Its a hack because gna_verifier seems to fail when too many names are sent at once including strange ones such as what is obtain whith rglobi. Only used if `valid_taxo_target_taxon` is set to TRUE.

Value

Either a tibble (if add_to_phyloseq = FALSE) or a new phyloseq object, if add_to_phyloseq = TRUE, with new column(s) in the tax_table.

Details

This function is mainly a wrapper of the work of others. Please cite `rglobi` and `taxize` packages.

Author

Adrien Taudiere

Examples

data_fungi_mini_cleanNames <- gna_verifier_pq(data_fungi_mini,
  data_sources = 210
)
#> ✔ GNA verification summary:
#> • Total taxa in phyloseq: 45
#> • Taxa submitted for verification: 37
#> • Genus-level only taxa: 2
#> • Total matches found: 25
#> • Synonyms: 4 (including 4 at genus level)
#> • Accepted names: 21 (including 15 at genus level)

data_fungi_mini_cleanNames <- tax_globi_pq(data_fungi_mini_cleanNames,
  interaction_types = c("hasHost")
)

# \donttest{
res_globi <- tax_globi_pq(data_fungi_mini,
  taxonomic_rank = c("Genus", "Species"),
  interaction_types = list("parasiteOf", "hasHost"),
  verbose = TRUE,
  max_interactions = 10
)
#> Error in if (discard_genus_alone) {    taxnames <- taxnames[grepl(pattern = " ", taxnames)]}: the condition has length > 1
# }