Add metadata to the tidytacos object — add

add_metadata() adds sample or taxon metadata to the sample or taxon table, respectively, of a tidytacos object.

Usage

add_metadata(ta, metadata, table_type = "sample")

Arguments

ta: A tidytacos object.
metadata: A tibble containing data for each sample or taxon. Samples/taxa should be rows, while metadata variables should be columns. At least one column name needs to be shared with the sample or taxa table of the tidytacos object. The default shared column name is 'sample' for samples and 'taxon' for taxa.
table_type: The type of table to add, either 'sample' or 'taxa'.

Value

A tidytacos object with the metadata added.

Examples

# Initiate counts matrix
x <- matrix(
  c(1500, 1300, 280, 356),
  ncol = 2
)
rownames(x) <- c("taxon1", "taxon2")
colnames(x) <- c("sample1", "sample2")

# Convert to tidytacos object
data <- create_tidytacos(x,
  taxa_are_columns = FALSE
)

# Initiate sample tibble
sample <- c("sample1", "sample2")
environment <- c("food fermentation", "human stool")
sample_tibble <- tibble::tibble(sample, environment)

# Add sample tibble to tidytacos object
data <- data %>%
  add_metadata(sample_tibble)
#> Joining with `by = join_by(sample)`

# Initiate taxon tibble
genera <- c("Lactobacillus", "Limosilactobacillus")
species <- c("crispatus", "reuteri")
taxonomy <- tibble::tibble(taxon = rownames(x), genera, species)

# Add taxon tibble to tidytacos object
data <- data %>%
  add_metadata(taxonomy, table_type = "taxa")
#> Joining with `by = join_by(taxon)`
#> Warning: Not all default rank names found. Replacing them with:
#>  c("genera","species")
#> 
#> If these are not the rank names of your taxon table in descending order, 
#> please set them manually using 'set_rank_names()'