Count unique taxonomic levels across phyloseq objects

Creates a summary table showing the number of unique taxonomic values (levels) for each taxonomic rank across all phyloseq objects in a list_phyloseq. This is useful for comparing taxonomic resolution and diversity across different datasets or classification methods.

Usage

n_levels_lpq(x, taxonomic_ranks, na.rm = TRUE)

Arguments

x

(required) A list_phyloseq object.

taxonomic_ranks

(character vector, required) Names of taxonomic ranks to count. Must be present in the tax_table of ALL phyloseq objects in the list.

na.rm

(logical, default TRUE) If TRUE, NA values are excluded when counting unique levels.

Value

A data frame with:

Rows

One row per phyloseq object (named by the phyloseq name)

Columns

One column per taxonomic rank, containing the count of unique values for that rank in that phyloseq object

See also

upset_lpq()

Author

Adrien Taudière

Examples

lpq <- list_phyloseq(list(fungi = data_fungi, fungi_mini = data_fungi_mini))
#> ℹ Building summary table for 2 phyloseq objects...
#> ℹ Computing comparison characteristics...
#> ℹ Checking sample and taxa overlap...
#> ℹ Detected comparison type: NESTED_ROBUSTNESS
#> ℹ 137 common samples, 45 common taxa
#> ✔ list_phyloseq created (NESTED_ROBUSTNESS)

n_levels_lpq(lpq, c("Phylum", "Class", "Order", "Family", "Genus"))
#>            Phylum Class Order Family Genus
#> fungi           6    25    73    163   252
#> fungi_mini      1     3     9     20    22