Format feature labels for dominant-feature assignments and dCSTs

Builds unique display labels from stable feature IDs and taxonomy strings. This is useful when dCST computation should operate on stable internal feature identifiers (for example asv_4) while reports and figures should use human-readable labels such as L. iners 4.

Underscores in taxonomy strings are converted to spaces before abbreviation and aliasing. If multiple features share the same display taxon, an index can be appended either from the global feature ID (for example asv_4 -> 4) or by within-taxon order.

Usage

linf.feature.labels(
  feature.ids,
  taxonomy,
  abbreviations = NULL,
  aliases = NULL,
  duplicate.index = c("global", "within_taxon", "none"),
  fallback.to.id = TRUE
)

Arguments

feature.ids

Character vector of stable feature identifiers.

taxonomy

Character vector of taxonomy strings, same length as feature.ids.

abbreviations

Optional named character vector mapping genus tokens to display abbreviations, for example c(Lactobacillus = "L.").

aliases

Optional named character vector mapping full taxonomy strings to alternate labels, for example c("Ca. Lachnocurva vaginae" = "BVAB1").

duplicate.index

One of "global", "within_taxon", or "none". Controls how duplicate display taxa are disambiguated.

fallback.to.id

Logical. If TRUE, missing taxonomy values fall back to the feature ID.

Value

Character vector of unique display labels.

Examples

ids <- c("asv_1", "asv_4", "asv_5", "asv_6")
tax <- c(
  "Lactobacillus iners",
  "Lactobacillus iners",
  "Megasphaera lornae",
  "Ca_Lachnocurva_vaginae"
)
abbr <- c(
  Lactobacillus = "L.",
  Gardnerella = "Gard.",
  Megasphaera = "Mega."
)
aliases <- c(
  "Ca. Lachnocurva vaginae" = "BVAB1",
  "Ca_Lachnocurva_vaginae" = "BVAB1"
)
linf.feature.labels(ids, tax, abbreviations = abbr, aliases = aliases)
#> [1] "L. iners 1"   "L. iners 4"   "Mega. lornae" "BVAB1"