View source: R/plot_functions.R
rotl_pq | R Documentation |
Make a phylogenetic tree using the ASV names of a physeq object and the Open Tree of Life tree.
rotl_pq(physeq, species_colnames = "Genus_species", context_name = "All life")
physeq |
(required): a |
species_colnames |
(default: "Genus_species"): the name of the column
where the species binominal name is stored in |
context_name |
: can bue used to select only a part of the Open Tree
of Life. See |
This function is mainly a wrapper of the work of others.
Please make a reference to rotl
package if you
use this function.
A plot
Adrien Taudière
if (requireNamespace("rotl")) {
tr <- rotl_pq(data_fungi_mini, species_colnames = "Genus_species")
plot(tr)
tr_Asco <- rotl_pq(data_fungi, species_colnames = "Genus_species", context_name = "Ascomycetes")
plot(tr_Asco)
}
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