tidypq

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

tidypq is not available on CRAN yet. You can install the stable development version from GitHub with:

# Install from GitHub (development version)
if (!require("devtools", quietly = TRUE)) {
  install.packages("devtools")
}
devtools::install_github("adrientaudiere/tidypq")
# Or using pak
# pak::pkg_install("adrientaudiere/tidypq")

You can install the unstable development version from GitHub with:

if (!require("devtools", quietly = TRUE)) {
  install.packages("devtools")
}
devtools::install_github("adrientaudiere/tidypq", ref = "dev")

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