Function to filter rows of a MetaPhlAn profile based on the selected taxonomic level. Used if profile not yet separated into taxonomic ranks.
Arguments
- df
A data frame. Assumes clade names are of the structure k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae and found in the 'clade_name' column.
- taxa_lvl
A
characterstring. The taxonomic level to extract ('kingdom', 'phylum', 'class', 'order', 'family', 'genus', 'species' or 't' (SGB)). First letter abbreviations (e.g., 's') are also accepted.
Examples
filtered_profile <- filter_taxa_lvl(merged_abundance_profiles, "Class")
head(filtered_profile)
#> clade_name SRS014459.Stool
#> 1 k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria 0
#> 2 k__Bacteria|p__Actinobacteria|c__Actinomycetia 0
#> 3 k__Bacteria|p__Firmicutes|c__Negativicutes 0
#> 4 k__Bacteria|p__Bacteroidota|c__Bacteroidia 0
#> 5 k__Bacteria|p__Firmicutes|c__Bacilli 0
#> SRS014464.Anterior_nares SRS014470.Tongue_dorsum SRS014472.Buccal_mucosa
#> 1 81.20128 0.00000 14.7449
#> 2 18.79872 0.00000 0.0000
#> 3 0.00000 74.02531 0.0000
#> 4 0.00000 25.97469 0.0000
#> 5 0.00000 0.00000 85.2551
#> SRS014476.Supragingival_plaque SRS014494.Posterior_fornix
#> 1 0.00000 0
#> 2 85.43048 0
#> 3 0.00000 0
#> 4 0.00000 0
#> 5 14.56952 100