metacoder (version 0.1.3)

taxon_data: Return taxon data from taxmap

Description

Return a table of data associated with taxa of and object of type taxmap.

Usage

taxon_data(obj, row_subset = NULL, col_subset = NULL,
  calculated_cols = TRUE, sort_by = NULL, decreasing = FALSE,
  drop = FALSE)

Arguments

obj

(taxmap)

row_subset

(character) The taxon_ids of a subset of obj. Default: All rows.

col_subset

(character) The names of columns, either user defined or generated using taxon_funcs. Default: All columns.

calculated_cols

(logical of length 1) If TRUE, return calculated columns using functions in taxmap$taxon_funcs. These values are calculated each time taxon_data is called since their values can change if the data is subset.

sort_by

(character of length 1) The name of a column in obj$taxon_data or a function name in obj$taxon_funcs. This column will be used to sort the output rows. If NULL, no sorting will be done.

decreasing

(logical of length 1) If TRUE, sort_by order is decreasing.

drop

(logical of length 1) If TRUE, if subset is a single column name, then a vector is returned instead of a data.frame

Value

A data.frame or vector with rows corresponding to taxa in input