Identify dominant taxa in each sample and give overview.
dominant_taxa(x, level = NULL, group = NULL)phyloseq-class object
Taxonomic level uses microbiome::aggregate_taxa
Provide overview by groups. Default=NULL
A list of two data frames/tibbles
Identifies the dominant taxa in each sample and gives an overview of frequency and percent sample that are dominated by each taxon. Can be group wise or overall.
library(microbiomeutilities)
library(dplyr)
data("zackular2014")
p0 <- zackular2014
x.d <- dominant_taxa(p0, level = "Genus", group = "DiseaseState")
head(x.d$dominant_overview)
#> # A tibble: 6 × 5
#> # Groups: DiseaseState [3]
#> DiseaseState dominant_taxa n rel.freq rel.freq.pct
#> <fct> <chr> <int> <dbl> <chr>
#> 1 H g__Bacteroides 15 50 50%
#> 2 nonCRC g__Blautia 13 46.4 46%
#> 3 CRC g__Bacteroides 9 30 30%
#> 4 CRC g__Blautia 9 30 30%
#> 5 H g__Blautia 7 23.3 23%
#> 6 nonCRC g__Bacteroides 6 21.4 21%