Coerce phyloseq objects to tibble data frames — as

These functions extend the as_tibble() function defined by the tibble package to work on phyloseq objects or phyloseq-component objects.

# S3 method for otu_table
as_tibble(x, pivot = TRUE, .name_repair = base::make.unique)

# S3 method for sample_data
as_tibble(x, .name_repair = base::make.unique)

# S3 method for taxonomyTable
as_tibble(x, .name_repair = base::make.unique)

# S3 method for XStringSet
as_tibble(x)

# S3 method for phyloseq
as_tibble(x, tax = TRUE, ref = FALSE, .name_repair = base::make.unique)

Arguments

x	A phyloseq object or component.
pivot	Whether to pivot the otu table to long format.
.name_repair	Function to repair names in the case of conflicts.
tax	Whether to include taxonomy data.
ref	Whether to include reference sequences.

Value

A tibble (tbl_df)

Details

Tibbles (tbl_df objects) do not support rownames; the taxa and sample names in the returned tibbles will always be stored in the first or second columns. The names ".otu", ".sample", ".abundance", and ".sequence" are special column names reserved for the otu/taxa names, sample names, abundances, and reference sequences.

Examples

library(tibble) # for as_tibble() and glimpse()

data(GlobalPatterns)

# Subset to 1/100 of the original taxa to speed operations
ps <- GlobalPatterns %>%
  filter_tax_table(dplyr::row_number() %% 100 == 1)
#> Error in filter_tax_table(., dplyr::row_number()%%100 == 1): could not find function "filter_tax_table"

# On phyloseq objects, as_tibble is similar to psmelt()
psmelt(ps) %>% glimpse
#> Error in psmelt(ps): object 'ps' not found
as_tibble(ps) %>% glimpse
#> Error in as_tibble(ps): object 'ps' not found

# By default, the otu_table method provides a tibble in long-format like
# psmelt and the phyloseq method
otu_table(ps) %>% as_tibble %>% glimpse
#> Error in h(simpleError(msg, call)): error in evaluating the argument 'object' in selecting a method for function 'otu_table': object 'ps' not found

# Sample data and taxonomy tables produced by as_tibble can be converted
# back into their respective phyloseq objects using speedyseq's tbl_df
# constructors
sample_data(ps) <- sample_data(ps) %>%
  as_tibble %>%
  dplyr::mutate(sample_sum = sample_sums(ps)) %>%
  sample_data
#> Error in h(simpleError(msg, call)): error in evaluating the argument 'object' in selecting a method for function 'sample_data': error in evaluating the argument 'object' in selecting a method for function 'sample_data': object 'ps' not found
sample_data(ps) %>% glimpse
#> Error in h(simpleError(msg, call)): error in evaluating the argument 'object' in selecting a method for function 'sample_data': object 'ps' not found