tax_rename: Make new phyloseq taxa names from classification and taxon...

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

Make new phyloseq taxa names from classification and taxon abundance info

Description

Pairs classification at the given rank with a numeric ranking suffix (based on abundance or prevalence data) to automatically create informative taxa names.

Usage

tax_rename(
  ps,
  rank,
  sort_by = sum,
  transform_for_sort = "identity",
  pad_digits = "auto",
  sep = " ",
  ...
)

Arguments

ps	phyloseq object
rank	name of rank to use in new taxa names
sort_by	how to sort taxa for numbering within rank-based groups (a tax_sort option)
transform_for_sort	named of transformation to apply to taxa before sorting
pad_digits	how long should the numeric suffixes be? see details
sep	character to separate the rank prefixes from numeric suffixes
...	additional arguments passed to tax_sort

Details

e.g. "Bacteroides 003" for the third most abundant Bacteroides OTU or ASV.

Taxa are returned in original order, and otu_table is returned un-transformed.

pad_digits options:

• "auto" –> minimum digits to have equal length numbers within groups

• "max" –> minimum digits to have equal length numbers across all groups

• A number: e.g.

  • 3 –> 001, 002, ..., 042, ..., 180, ...

  • 1 –> 1, 2, ..., 42, ..., 180, ...

Value

phyloseq object

See Also

phyloseq::taxa_names for accessing and manually setting names

Examples

library(phyloseq)
data("ibd", package = "microViz")

ps <- ibd %>%
  tax_filter(min_prevalence = 3) %>%
  tax_fix()

# show a few of the current, uninformative names
taxa_names(ps) %>% head(15)
taxa_names(ps) %>% tail(15)

# change names to genus classification plus number
psNewNames <- ps %>% tax_rename(rank = "Genus")

taxa_names(psNewNames) %>% head(15)
taxa_names(psNewNames) %>% tail(15)

# demonstrate some alternative argument settings
psNewNames2 <- ps %>% tax_rename(
  rank = "Family", sort_by = prev, pad_digits = "max", sep = "-"
)

taxa_names(psNewNames2) %>% head(15)
taxa_names(psNewNames2) %>% tail(15)

ps %>%
  tax_rename(rank = "Genus", pad_digits = 2) %>%
  taxa_names() %>%
  head(15)

# naming improvement on plots example
library(ggplot2)
library(patchwork)

# Overly aggressive OTU filtering to simplify and speed up example
psExample <- ps %>% tax_filter(min_prevalence = 0.4)

# before OTU renaming
before <- psExample %>%
  ps_filter(activity == "inactive") %>%
  tax_names2rank("Taxon") %>%
  comp_barplot(
    tax_level = "Taxon", n_taxa = 12, other_name = "Other",
    merge_other = FALSE, bar_outline_colour = "grey60"
  ) +
  coord_flip() +
  ggtitle("Original taxon names :(")

# after OTU renaming
after <- psExample %>%
  ps_filter(activity == "inactive") %>%
  tax_rename(rank = "Genus", pad_digits = "max") %>%
  tax_names2rank("Taxon") %>%
  comp_barplot(
    tax_level = "Taxon", n_taxa = 12, other_name = "Other",
    merge_other = FALSE, bar_outline_colour = "grey60"
  ) +
  coord_flip() +
  ggtitle("New taxon names :)", "tax_rename(rank = 'Genus', sort_by = sum)")

before + after & theme(legend.text = element_text(size = 8))

# ordination example
psExample %>%
  tax_rename(rank = "Genus", sort_by = sum) %>%
  tax_names2rank("otu") %>%
  tax_transform("clr", rank = "otu") %>%
  ord_calc() %>%
  ord_plot(
    size = 2, colour = "ibd", shape = "circle", alpha = 0.5,
    plot_taxa = 1:10,
    tax_vec_length = 0.5,
    tax_lab_style = tax_lab_style(
      type = "text", max_angle = 90, check_overlap = TRUE,
      size = 2.5, fontface = "bold"
    ),
    tax_vec_style_all = vec_tax_all(alpha = 0.1)
  ) +
  coord_fixed(clip = "off") +
  stat_chull(aes(colour = ibd)) +
  scale_colour_brewer(palette = "Dark2") +
  theme(panel.grid = element_line(size = 0.1))

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