Compute intra-taxanames distances for each taxa names

This function computes intra-taxanames distances for each taxonomic names (e.g. Genus species) in a phyloseq object containing ASV/OTU sequences and taxonomy.

The distances are computed using the DECIPHER package, which aligns the sequences (`DECIPHER::AlignSeqs()`) and calculates a distance matrix (`DECIPHER::DistanceMatrix()`).

Usage

intra_taxnames_dist(
  physeq,
  taxonomic_rank = c("Genus", "Species"),
  verbose = TRUE,
  verbose_DECIPHER = FALSE,
  discard_NA = TRUE,
  ...
)

Arguments

physeq

A phyloseq object containing ASV/OTU sequences and refseq

taxonomic_rank

Character. Name of the taxonomy column(s) containing taxonomic assignments to compute intra-taxa distances. Can be a vector of two columns (e.g. c("Genus", "Species"), the default).

verbose

Logical. Print progress messages (default: TRUE)

verbose_DECIPHER

Logical. If TRUE, print messages from DECIPHER functions (default: FALSE)

...

Additional arguments to pass to `DECIPHER::AlignSeqs()`

Value

A data.frame with columns: - taxnames: taxonomic names - n_taxa: number of taxa assigned to this taxnames - mean_dist: mean intra-taxanames distance - min_dist: minimum intra-taxanames distance - max_dist: maximum intra-taxanames distance

See also

[DECIPHER::AlignSeqs()], [DECIPHER::DistanceMatrix()]

Author

Adrien Taudiere

Examples

intra_taxn_dist <- intra_taxnames_dist(data_fungi_mini)
#> ✔ Processing Stereum ostrea - 3 taxa
#> ✔ Processing Xylodon raduloides - 3 taxa
#> ✔ Processing Ossicaulis lachnopus - 4 taxa
#> ℹ  Stereum hirsutum is represented by only one taxa
#> ℹ  Antrodiella brasiliensis is represented by only one taxa
#> ℹ  Basidiodendron eyrei is represented by only one taxa
#> ℹ  Sistotrema oblongisporum is represented by only one taxa
#> ✔ Processing Fomes fomentarius - 4 taxa
#> ℹ  Mycena renati is represented by only one taxa
#> ℹ  Helicogloea pellucida is represented by only one taxa
#> ℹ  Radulomyces molaris is represented by only one taxa
#> ℹ  Elmerina caryae is represented by only one taxa
#> ℹ  Phanerochaete livescens is represented by only one taxa
#> ℹ  Gloeohypochnicium analogum is represented by only one taxa
#> ℹ  Hyphoderma roseocremeum is represented by only one taxa
#> ℹ  Hyphoderma setigerum is represented by only one taxa
#> ℹ  Trametes versicolor is represented by only one taxa
#> ℹ  Peniophora versiformis is represented by only one taxa
#> ✔ Processing Exidia glandulosa - 2 taxa
#> ℹ  Peniophorella pubera is represented by only one taxa
#> ℹ  Auricularia mesenterica is represented by only one taxa
#> ℹ  Marchandiomyces buckii is represented by only one taxa
#> ℹ  Hericium coralloides is represented by only one taxa
#> ℹ  Xylodon flaviporus is represented by only one taxa
#> ✔ Intra-taxnames distance computation complete
#> ℹ Total taxnames: 24
#> ℹ Taxnames with only one taxa (no distance computation):  19
#> ℹ Taxnames with multiple taxa: 5
#> ℹ Mean intra-taxnames mean distance: 0.006
#> ℹ Mean intra-taxnames maximum distance: 0.0087
#> ℹ Mean intra-taxnames minimum distance: 0.0035
plot(intra_taxn_dist$mean_dist, intra_taxn_dist$n_taxa)

plot(intra_taxn_dist$min_dist, intra_taxn_dist$n_taxa)

plot(intra_taxn_dist$max_dist, intra_taxn_dist$n_taxa)