ps_calc_richness: Calculate richness estimate and add to phyloseq sample data

In david-barnett/microViz: Microbiome Data Analysis and Visualization

Calculate richness estimate and add to phyloseq sample data

Description

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

Usage

ps_calc_richness(
  ps,
  rank,
  index = "observed",
  detection = 0,
  varname = paste0(index, "_", rank)
)

Arguments

ps	phyloseq
rank	taxonomic rank name, or "unique"
index	"observed" or "chao1" - name of richness estimate from microbiome::richness()
detection	Detection threshold. Used for the "observed" index.
varname	name of the variable to be added to phyloseq sample data

Details

Don't filter taxa before calculating richness.

These richness indices are estimates. For a discussion of the uncertainty and bias of these estimates see e.g. work by Amy Willis https://doi.org/10.3389/fmicb.2019.02407

Value

phyloseq

See Also

ps_calc_diversity

microbiome::richness

Examples

data(ibd, package = "microViz")
ibd %>%
  ps_filter(abx == "abx") %>%
  tax_fix() %>%
  ps_calc_richness("Genus", index = "observed") %>%
  ps_calc_richness("Family", index = "chao1") %>%
  tax_transform(rank = "Genus", transform = "clr") %>%
  ord_calc("PCA") %>%
  ord_plot(
    colour = "observed_Genus", size = "chao1_Family"
  ) +
  ggplot2::scale_colour_viridis_c()

david-barnett/microViz documentation built on April 17, 2025, 4:25 a.m.