Plot the taxa occurrence using gbif.range package

A wrapper of [gbif.range::get_gbif()] function to plot the range of taxa using ggplot2. The function can take either a phyloseq object or a vector of taxonomic names. If a phyloseq object is provided, the taxonomic names are extracted from the specified taxonomic rank. The occurrences are plotted either as points or using hexagonal binning. The function can also filter the occurrences by country.

Usage

plot_tax_gbif_pq(
  physeq = NULL,
  taxnames = NULL,
  taxonomic_rank = "currentCanonicalSimple",
  interactive_plot = FALSE,
  zcol = c("year", "taxonomicStatus"),
  hexagons = FALSE,
  bins = 100,
  verbose = TRUE,
  countries = NULL,
  info_names = c("country", "country code", "acceptedScientificName", "ScientificName"),
  discard_genus_alone = identical(taxonomic_rank, "currentCanonicalSimple"),
  discard_NA = TRUE,
  ...
)

Arguments

physeq: (optional) A phyloseq object
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")).
interactive_plot: (logical, default FALSE) If TRUE, an interactive map is created using the package mapview.
zcol: (character vector, default c("year", "taxonomicStatus")) Only used if interactive_plot is TRUE. The column(s) of the occurrences to use for coloring the points in the interactive map. See ?mapview::mapview() for more details.
hexagons: (logical, default FALSE) Only used if interactive_plot is FALSE. If TRUE, use hexagonal binning to plot the occurrences. If FALSE, plot the occurrences as points.
bins: (Number of bins for hexagonal binning, default 100) Only used if hexagons is TRUE and interactive_plot is FALSE.
verbose: (logical, default TRUE) If TRUE, prompt some messages.
countries: A character vector of country names to filter the occurrences. If NULL (default), all countries are used (no filter).
info_names: (Character vector) The information to retrieve from GBIF for each occurrence. See [gbif.range::get_gbif()] for more details.
discard_genus_alone: (logical, default `TRUE` when `taxonomic_rank == "currentCanonicalSimple"`). Passed to [taxonomic_rank_to_taxnames()].
discard_NA: (logical, default `TRUE`). Passed to [taxonomic_rank_to_taxnames()].
...: Additional arguments to pass to [gbif.range::get_gbif()].

Value

A list of ggplot2 objects, one for each taxon.

Author

Adrien Taudiere

Examples

if (FALSE) { # \dontrun{
data_fungi_mini_cleanNames <- gna_verifier_pq(data_fungi_mini, data_sources = 210)

p <- plot_tax_gbif_pq(
  subset_taxa_pq(
    data_fungi_mini_cleanNames,
    taxa_sums(data_fungi_mini) > 20000
  ),
  hexagons = TRUE,
  verbose = TRUE, bins = 50, occ_samp = 100, grain = 10000
)

p <- plot_tax_gbif_pq(taxnames = c("Xylobolus subpileatus", "Stereum subpileatus"))

p <- plot_tax_gbif_pq(taxnames = c("Stereum ostrea", "Mycena renati"))
requireNamespace("patchwork")
p[[1]] / p[[2]] & no_legend()


p <- plot_tax_gbif_pq(
  taxnames = c("Xylobolus subpileatus", "Stereum  subpileatus"),
  hexagons = TRUE, verbose = FALSE
)

p <- plot_tax_gbif_pq(
  taxnames = c("Xylobolus subpileatus", "Stereum subpileatus"),
  hexagons = TRUE, verbose = FALSE, countries = c("france", "spain")
)

p[[1]] + coord_fixed(ylim = c(30, 50), xlim = c(-5, 25)) + no_legend()

p <- plot_tax_gbif_pq(
  taxnames = c(
    "Ossicaulis lachnopus",
    "Antrodiella brasiliensis",
    "Stereum ostrea",
    "Xylobolus subpileatus"
  ),
  hexagons = TRUE,
  verbose = F, bins = 50, occ_samp = 100, grain = 10000
)

requireNamespace("patchwork")
(p[[1]] + p[[2]]) /
  (p[[3]] + p[[4]]) & no_legend()
} # }

Usage

Arguments

Value

See also

Author

Examples