Summarize Taxonomic Assignments

Summarize Taxonomic Assignments

summarizeTaxonomicAssignments(x)

Arguments

x

A phyloseq object

Value

tibble with overview of taxonomic assignments.

Details

Percentage of taxa that have been assigned to the different taxonomic levels. Non assigned levels must be NA. Check biomeUtils::cleanTaxonomy.

Author

Sudarshan A. Shetty

Examples

library(biomeUtils)
data("SprockettTHData")
# run cleanTaxonomy if special characters are
# present in tax_table
summarizeTaxonomicAssignments(SprockettTHData)
#> In Species column- 156 are ambigous assignments
#> # A tibble: 7 × 4
#>   Ranks   TaxonomyAssigned Total PrecentAssigned
#>   <chr>              <int> <int>           <dbl>
#> 1 Kingdom             2319  2319           100  
#> 2 Phylum              2313  2319            99.7
#> 3 Class               2308  2319            99.5
#> 4 Order               2298  2319            99.1
#> 5 Family              2067  2319            89.1
#> 6 Genus               1734  2319            74.8
#> 7 Species              482  2319            20.8