ps_calc_dominant: Calculate dominant taxon in each phyloseq sample

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

Calculate dominant taxon in each phyloseq sample

Description

Which taxon is most abundant in each sample of your phyloseq object? This function adds this information as a new variable in your phyloseq sample_data.

• If the most abundant taxon is below the proportional abundance threshold, the dominant taxon will be "none" for that sample

• If there are more than n_max dominant taxa across all samples (not including "none") the dominant taxon will be "other" for those samples

Usage

ps_calc_dominant(
  ps,
  rank,
  threshold = 0.3,
  n_max = 6,
  var = paste("dominant", rank, sep = "_"),
  none = "none",
  other = "other"
)

Arguments

ps	phyloseq object
rank	taxonomic rank to calculate dominance at
threshold	minimum proportion at which to consider a sample dominated by a taxon
n_max	maximum number of taxa that can be listed as dominant taxa
var	name of variable to add to phyloseq object sample data
none	character value to use when no taxon reaches threshold
other	character value to use when another taxon (>n_max) dominates

Details

Thanks to Vitor Heidrich for the idea and a draft implementation

Value

phyloseq object

Examples

library(ggplot2)
ps <- microViz::ibd %>%
  tax_filter(min_prevalence = 3) %>%
  tax_fix() %>%
  phyloseq_validate()

ps %>%
  ps_filter(DiseaseState == "CD") %>%
  ps_calc_dominant(rank = "Genus") %>%
  comp_barplot(tax_level = "Genus", label = "dominant_Genus", n_taxa = 12) +
  coord_flip()

ps %>%
  ps_calc_dominant(rank = "Genus") %>%
  tax_transform(rank = "Genus", trans = "clr") %>%
  ord_calc("PCA") %>%
  ord_plot(colour = "dominant_Genus", size = 3, alpha = 0.6) +
  scale_colour_brewer(palette = "Dark2")

# customise function options
ps %>%
  ps_calc_dominant(
    rank = "Family", other = "Other", none = "Not dominated",
    threshold = 0.4, n_max = 3
  ) %>%
  tax_transform(rank = "Genus", trans = "clr") %>%
  ord_calc("PCA") %>%
  ord_plot(colour = "dominant_Family", size = 3, alpha = 0.6) +
  scale_colour_manual(values = c(
    Bacteroidaceae = "forestgreen", Lachnospiraceae = "darkblue",
    Ruminococcaceae = "darkorange", Other = "red", "Not dominated" = "grey"
  ))

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