make_taxon_labels: Make labels summarizing the taxonomy of each sequence

In brendanf/phylotax: Refine taxonomic assignment of environmental sequences using a taxonomic tree

Description

Make labels summarizing the taxonomy of each sequence

Usage

make_taxon_labels(t, cols = character(), abbrev = FALSE)

Arguments

t	(data.frame) Taxonomy assignments to summarize. At a minimum, should include columns "label", "rank", and "taxon".
cols	(character) (optional) Additional columns from t which will be included in the output. They should be identical for each value of "label".
abbrev	(logical or data.frame) If TRUE, use a standard set of abbreviations for mycological taxon names. Alternatively, define your own abbreviations using a data.frame with columns "pattern" and "replacement", which are passed on to gsub().

Details

The standard abbreviations are:

pattern	replacement
(mycota|mycetes|ales|aceae)
incertae_sedis	i_s
Fungi\b	F
Basidio\b	B
Asco\b	A
Chytridio\b	Chy
Mucoro\b	Muc
Glomero\b	Glo

Value

A data.frame giving the old and new taxon taxon labels.

brendanf/phylotax documentation built on March 3, 2021, 2:21 p.m.