Add absolute abundances to count table

add_absolute_abundance() calculates absolute abundances of taxa in samples given a taxon that was spiked into all of the samples during library prep. The function then adds these absolute abundances to the count table of the tidytacos object under the column name "absolute_abundance".

Usage

add_absolute_abundance(ta, spike_taxon, spike_added = spike_added)

Arguments

ta

A tidytacos object.

spike_taxon

The taxon id of the spike.

spike_added

The column name in the sample table which indicates how much spike was added per sample.

Value

A tidytacos object with absolute abundances added to the count table.

See also

Other count-modifiers: add_density(), add_rel_abundance()

Examples

# Initiate count matrix
x <- matrix(
  c(1500, 1300, 14, 280, 356, 9),
  ncol = 2
)
rownames(x) <- c("taxon1", "taxon2", "taxon3")
colnames(x) <- c("sample1", "sample2")

# Convert to tidytacos object
data <- create_tidytacos(x,
  taxa_are_columns = FALSE
)
data$samples$spike_added <- c(100, 150)

# Add total abundance
data <- data %>%
  add_absolute_abundance(spike_taxon = "t3")