Add FungalTraits and FUNGuild information to a phyloseq object
Source:R/fungal_traits_guilds.R
fungal_traits_guilds.Rd<a href="https://adrientaudiere.github.io/MiscMetabar/articles/Rules.html#lifecycle"> <img src="https://img.shields.io/badge/lifecycle-maturing-blue" alt="lifecycle-maturing"></a>
A convenience wrapper that adds guild and trait information from both the FungalTraits database and the FUNGuild database to the `tax_table` slot of a phyloseq object. Optionally creates consensus columns that summarise agreement between the two databases.
If `currentCanonicalSimple` is not already present in the `tax_table`, [gna_verifier_pq()] is called internally to clean and verify the taxonomic names before querying the databases.
Usage
fungal_traits_guilds(
physeq,
fungal_traits_file = system.file("extdata", "fungal_traits.csv", package = "taxinfo"),
ft_taxonomic_rank = "genusEpithet",
ft_csv_rank = "GENUS",
ft_sep = "\t",
ft_col_prefix = "ft_",
fg_tax_levels = c("Kingdom", "Phylum", "Class", "Order", "Family", "Genus", "Species"),
fg_col_prefix = "fg_",
ft_csv_cols_select = c("GENUS", "COMMENT.on.genus", "primary_lifestyle",
"Secondary_lifestyle", "Comment_on_lifestyle_template",
"Endophytic_interaction_capability_template", "Plant_pathogenic_capacity_template",
"Decay_substrate_template", "Decay_type_template", "Aquatic_habitat_template",
"Animal_biotrophic_capacity_template", "Specific_hosts", "Growth_form_template",
"Fruitbody_type_template", "Hymenium_type_template",
"Ectomycorrhiza_exploration_type_template", "Ectomycorrhiza_lineage_template",
"primary_photobiont",
"secondary_photobiont"),
db_url = "http://www.stbates.org/funguild_db_2.php",
add_consensus = TRUE,
consensus_col_prefix = "cons_",
add_to_phyloseq = TRUE,
gna_data_sources = c(1, 12),
verbose = TRUE
)Arguments
- physeq
A phyloseq object.
- fungal_traits_file
(Character) Path to the FungalTraits CSV file. Defaults to the simplified version bundled with the package.
- ft_taxonomic_rank
(Character, default `"genusEpithet"`) Column in `tax_table` used to match against the FungalTraits genus column.
- ft_csv_rank
(Character, default `"GENUS"`) Column in the FungalTraits CSV file that contains genus names.
- ft_sep
(Character, default `";"`) Field separator of the FungalTraits CSV file. See [utils::read.csv()].
- ft_col_prefix
(Character, default `"ft_"`) Prefix applied to all columns imported from FungalTraits.
- fg_tax_levels
(Character vector) Names of the tax_table columns that represent the 7 standard taxonomic ranks fed to FUNGuild.
- fg_col_prefix
(Character, default `"fg_"`) Prefix applied to all columns imported from FUNGuild.
- ft_csv_cols_select
A character vector of the column names to select from the FungalTraits CSV file.
- db_url
(Character) URL of the FUNGuild database. See [MiscMetabar::get_funguild_db()].
- add_consensus
(Logical, default `TRUE`) If `TRUE`, add consensus columns comparing trophic modes assigned by the two databases.
- consensus_col_prefix
(Character, default `"cons_"`) Prefix applied to consensus columns.
- add_to_phyloseq
(Logical, default `TRUE`) If `TRUE`, return an updated phyloseq object. If `FALSE`, return a tibble of the tax_table.
- gna_data_sources
Integer or character vector passed to [gna_verifier_pq()] when taxonomic names need to be verified. See [taxize::gna_verifier()].
- verbose
(Logical, default `TRUE`) If `TRUE`, print progress messages.
Value
Either an updated phyloseq object (when `add_to_phyloseq = TRUE`) or a tibble of the augmented tax_table.