Tidyverse-style verbs for manipulating phyloseq objects at four scales: samples, taxa, occurrences, and tree.
Function Naming Convention
All functions follow the pattern: {verb}_{scale}_pq()
| Verb | samples | taxa | occurrences | tree |
|---|---|---|---|---|
| filter | filter_samples_pq |
filter_taxa_pq |
filter_occurrences_pq |
filter_tree_pq |
| select | select_samdata_pq |
select_taxa_pq |
- | - |
| mutate | mutate_samdata_pq |
mutate_taxa_pq |
mutate_occurrences_pq |
- |
| slice | slice_samples_pq |
slice_taxa_pq |
- | - |
| arrange | arrange_samples_pq |
arrange_taxa_pq |
- | - |
| rename | rename_samples_pq |
rename_taxa_pq |
- | - |
Helper: taxa_prevalence(physeq, threshold)
Installation
# Install from GitHub
devtools::install_github("adrientaudiere/tidypq")Usage
library(tidypq)
library(MiscMetabar)
# Use the `.` pronoun to refer to the phyloseq object
data_fungi |>
filter_samples_pq(Height == "Low", sample_sums(.) > 1000) |>
filter_taxa_pq(taxa_sums(.) > 100) |>
mutate_samdata_pq(log_depth = log(sample_sums(.))) |>
mutate_occurrences_pq(. / sample_total) # Relative abundance