tax_reorder: Reorder taxa in phyloseq object using vector of names

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

Reorder taxa in phyloseq object using vector of names

Description

Reorder taxa in phyloseq object using vector of names

Usage

tax_reorder(
  ps,
  tax_order,
  tree_warn = TRUE,
  unmatched_warn = TRUE,
  ignore = c("other", "Other")
)

Arguments

ps	phyloseq object
tax_order	Names of taxa in desired order; at least some must match. (Numerical indices are also possible)
tree_warn	If phylogenetic tree is present in phyloseq phy_tree slot, taxa cannot be reordered. Default behaviour of tax_sort is to remove the phylogenetic tree and warn about this. tree_warn = FALSE will suppress the warning message, but still remove the tree!
unmatched_warn	Warn if any names (or indices) given in tax_order are not found within (range of) taxa_names(ps) - these will be ignored
ignore	Values that you do not want to be used for reordering taxa (useful for comp_barplot when custom palette names are used to set tax_order)

Value

phyloseq object (always without phy_tree)

Examples

data("dietswap", package = "microbiome")
new_order <- c(
  "Fusobacteria", "Cyanobacteria", "Verrucomicrobia", "Spirochaetes",
  "Actinobacteria", "Firmicutes", "Proteobacteria", "Bacteroidetes"
)
tax_agg(dietswap, rank = "Phylum") %>%
  ps_get() %>%
  phyloseq::taxa_names()

tax_agg(dietswap, rank = "Phylum") %>%
  ps_get() %>%
  tax_reorder(tax_order = new_order) %>%
  phyloseq::taxa_names()

# partial reordering (of the frontmost positions only) is possible
tax_agg(dietswap, rank = "Phylum") %>%
  ps_get() %>%
  tax_reorder(tax_order = c("Cyanobacteria", "Bacteroidetes")) %>%
  phyloseq::taxa_names()

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