assign_concise_taxonomy: Get concise taxonomic labels for microbes

In kimberlyroche/ROL: What the package does (short line)

Description

Get concise taxonomic labels for microbes

Usage

assign_concise_taxonomy(
  tax_level = "ASV",
  logratio = "alr",
  other_category = 0
)

Arguments

tax_level	taxonomic level at which to agglomerate data
logratio	logratio representation to use (e.g. "alr", "clr", "none")
other_category	"Other" taxonomic category of collapsed low abundance taxa (if available)

Details

If other_category is provided, these taxa will be rendered as *LR(Other).

Value

readable list of taxonomic labels (e.g. of the form "CLR(phylum Tenericutes)")

Examples

tax_labels <- assign_concise_taxonomy(tax_level="ASV", logratio="alr", other_category=0)

kimberlyroche/ROL documentation built on Dec. 10, 2020, 2:18 a.m.