Extract a canonical count table from a recipe
Value
A wide tibble with one row per taxon, taxa_id first, and one
column per sample. Taxa and samples follow phyloseq::taxa_names() and
phyloseq::sample_names() regardless of the stored OTU-table orientation.
Examples
data(metaHIV_phy)
rec <- recipe(metaHIV_phy)
otu_table(rec)
#> # A tibble: 451 × 157
#> taxa_id Sample_186 Sample_185 Sample_184 Sample_182 Sample_181 Sample_170
#> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 Otu_1 2538 0 9026 12049 22126 15374
#> 2 Otu_2 0 0 0 609 2543 988
#> 3 Otu_3 0 0 0 0 0 0
#> 4 Otu_4 0 0 0 0 0 0
#> 5 Otu_5 0 0 0 0 0 0
#> 6 Otu_6 0 0 0 0 0 0
#> 7 Otu_7 0 0 0 0 0 0
#> 8 Otu_8 0 0 0 0 0 0
#> 9 Otu_9 0 0 0 0 0 351
#> 10 Otu_10 0 0 10575 10764 504 0
#> # ℹ 441 more rows
#> # ℹ 150 more variables: Sample_169 <dbl>, Sample_168 <dbl>, Sample_167 <dbl>,
#> # Sample_166 <dbl>, Sample_165 <dbl>, Sample_164 <dbl>, Sample_163 <dbl>,
#> # Sample_162 <dbl>, Sample_160 <dbl>, Sample_159 <dbl>, Sample_158 <dbl>,
#> # Sample_157 <dbl>, Sample_156 <dbl>, Sample_155 <dbl>, Sample_153 <dbl>,
#> # Sample_152 <dbl>, Sample_151 <dbl>, Sample_150 <dbl>, Sample_149 <dbl>,
#> # Sample_148 <dbl>, Sample_147 <dbl>, Sample_146 <dbl>, Sample_145 <dbl>, …