add_density() adds densities (bacterial biomass per sample mass or
volume) to the count table of a tidytacos object under the column name
"density". Can only be used of a taxon was spiked into samples during library prep.
Usage
add_density(
ta,
spike_taxon,
spike_added = spike_added,
material_sampled = material_sampled
)Arguments
- ta
A tidytacos object.
- spike_taxon
The taxon id of the spike.
- spike_added
The column name of the sample table which indicates how much spike was added per sample, e.g. 16S rRNA gene copy numbers added to the DNA extraction tube.
- material_sampled
The column name indicating the amount of material from which DNA was extracted, e.g gram of soil. This parameter encourages researchers to consider that absolute abundances are only meaningful if they can be translated into densities.
See also
Other count-modifiers:
add_absolute_abundance(),
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)
data$samples$grams_source <- c(4, 5)
# Add density
data <- data %>%
add_density(spike_taxon = "t3", material_sampled=grams_source)