Initiate tidytacos object

create_tidytacos() returns a tidytacos object given a numeric matrix.

Usage

create_tidytacos(counts_matrix, taxa_are_columns = TRUE)

Arguments

counts_matrix

Numerical matrix containing the count data.

taxa_are_columns

A logical scalar. Are the taxa defined in columns?

Value

A tidytacos object.

Details

This function initiates a tidytacos object based on a numeric matrix. It will automatically create a dummy taxa table and sample table which will need to be updated using the function add_metadata(). When the taxa table is updated, the rank names can be set using the function set_rank_names() to make the tidytacos object aware of the taxonomy level order (from high to low). The taxa table should contain at the very least one rank name. The default rank names used by tidytacos are "domain", "phylum", "class", "order", "family", "genus" and "species".

See also

Other import-methods: from_dada(), from_phyloseq(), read_tidytacos()

Examples

# Initiate count 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
)
# Add taxonomy information
taxonomy <- tibble::tibble(
  taxon = c("taxon1", "taxon2"),
  domain = c("Bacteria", "Bacteria"),
  phylum = c("Bacillota", "Pseudomonadota"),
  class = c("Bacilli", "Gammaproteobacteria"),
  order = c("Lactobacillales", "Enterobacteriales"),
  family = c("Lactobacillaceae", "Enterobacteriaceae"),
  genus = c("Lactobacillus", "Escherichia"),
  species = c("Lactobacillus crispatus", "Escherichia coli")
)

data <- add_metadata(data, taxonomy, table_type = "taxa")
#> Joining with `by = join_by(taxon)`
# rank names are inferred from the taxa table, but can be set manually
# if we're not happy with the inferred rank names.
data <- set_rank_names(
  data, c("domain", "phylum", "class", "order", "family", "genus")
)