Find photos of taxa from GBIF or Wikitaxa

Usage

tax_photos_pq(
  physeq = NULL,
  taxnames = NULL,
  taxonomic_rank = "currentCanonicalSimple",
  source = "gbif",
  folder_name = "photos_physeq",
  add_to_phyloseq = NULL,
  col_prefix = NULL,
  gallery = FALSE,
  overwrite_folder = FALSE,
  col_name_url = "photo_url",
  verbose = TRUE,
  caption_valign = "bottom",
  caption_font_size = 12,
  simple_caption = FALSE,
  img_height = "150px",
  img_width = "200px",
  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. the c("Genus", "Species")).
source: (Character) either "gbif" or "wikitaxa".
folder_name: (default "photos_physeq") Name of the folder where photos will be downloaded. Only used if both add_to_phyloseq and gallery are FALSE.
add_to_phyloseq: (logical, default TRUE when physeq is provided, FALSE when taxnames is provided) If TRUE, a new phyloseq object is returned with a new column containing the URL (entitled with the parameter col_name_url) in the tax_table. 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).
gallery: (logical, default FALSE) If TRUE, a html gallery is created using [htmltools::browsable()].
overwrite_folder: (logical, default FALSE) If TRUE, the folder specified in the parameter folder_name will be deleted if it already exists.
col_name_url: (default "photo_url") Name of the new column in the tax_table
verbose: (logical, default TRUE) If TRUE, prompt some messages.
caption_valign: (character, default "bottom") Vertical alignment of the caption in the gallery. Either `"bottom"` or `"top"`.
caption_font_size: (int) Size of the caption font in the gallery.
simple_caption: (logical, default FALSE) If TRUE, the caption of the gallery photo will be only the taxonomic name. If FALSE, the caption include information from the phyloseq object (number of sequences, taxa and samples).
img_height: (character, default "150px") Height of images in the gallery.
img_width: (character, default "200px") Width of images in the gallery.
...: Unused, kept for backward compatibility.

Value

There is three behavior.(i) If add_to_phyloseq = TRUE, a new phyloseq object is returned with a new column (called with the parameter col_name_url) in the tax_table containing the URL; the gallery is printed as a side-effect if `gallery = TRUE`. (ii) If add_to_phyloseq = FALSE and gallery = TRUE, the HTML gallery is returned. (iii) If both gallery = FALSE and add_to_phyloseq = FALSE, photos are downloaded in a folder (folder_name parameter) and the list of url are returned in the form of a tibble.

Details

There is three behavior. See the returns section. Gbif source is quicker than wikitaxa source. Note that for the moment the function only return one photo per species.

Author

Adrien Taudiere

Examples

if (FALSE) { # \dontrun{
data_fungi_mini_cleanNames <- gna_verifier_pq(data_fungi_mini)

tax_photos_pq(data_fungi_mini_cleanNames,
  gallery = TRUE,
  img_height = "40px",
  img_width = "80px",
  source = "wikitaxa"
)

tax_photos_pq(
  taxnames = c("Xylodon flaviporus", "Basidiodendron eyrei"),
  gallery = TRUE
)

data_fungi_mini_cleanNames_photos <-
  tax_photos_pq(data_fungi_mini_cleanNames)

# Which photo(s) depicted more than one OTU
data_fungi_mini_cleanNames_photos@tax_table[, "photo_url"] |>
  table() |>
  (\(tab) tab[as.numeric(tab) > 1])()
} # }