Calculate diversity index and add to phyloseq sample data

Source: R/ps_calc_diversity.R

Wrapper around microbiome::diversity() function. Takes and returns a phyloseq object. Calculates an alpha diversity index at a given taxonomic rank. Returns phyloseq unaggregated, with an additional variable. Variable name is by default created by pasting the index and rank.

ps_calc_diversity(
  ps,
  rank,
  index = "shannon",
  exp = FALSE,
  varname = paste0(ifelse(exp, "exp_", ""), paste0(index, "_", rank))
)

Arguments

ps

phyloseq

rank

taxonomic rank name, or "unique"

index

name of diversity index from microbiome::diversity(). One of: "inverse_simpson", "gini_simpson", "shannon", "fisher", "coverage"

exp

exponentiate the result? (i.e. return e^index) - see details

varname

name of the variable to be added to phyloseq sample data

Value

phyloseq

Details

Don't filter taxa before calculating alpha diversity.

See the following resources for a discussion of exponentiated diversity indices http://www.loujost.com/Statistics%20and%20Physics/Diversity%20and%20Similarity/Diversity%20of%20a%20single%20community.htm http://www.loujost.com/Statistics%20and%20Physics/Diversity%20and%20Similarity/EffectiveNumberOfSpecies.htm

Examples

data(ibd, package = "microViz")
ibd %>%
  ps_filter(abx == "abx") %>%
  tax_fix() %>%
  ps_calc_diversity("Genus", index = "shannon", exp = TRUE) %>%
  ps_calc_diversity("Family", index = "inverse_simpson") %>%
  tax_transform(rank = "Genus", transform = "clr") %>%
  ord_calc("PCA") %>%
  ord_plot(
    colour = "exp_shannon_Genus", size = "inverse_simpson_Family"
  ) +
  ggplot2::scale_colour_viridis_c()
#> Warning: `transformation` argument deprecated, use `trans` instead.