get_taxmap_data: Get a data set from a taxmap object

In grunwaldlab/metacoder: Tools for Parsing, Manipulating, and Graphing Taxonomic Abundance Data

Get a data set from a taxmap object

Description

NOTE: This will be replaced by the function 'get_dataset' in the 'taxa' package. Get a data set from a taxmap object and complain if it does not exist. This is intended to be used to parse options in other functions.

Usage

get_taxmap_data(obj, data)

Arguments

obj	A taxmap object
data	Which data set to use. Can be any of the following: Name The name of the data set to use. Index The index of the data set to use. TRUE/FALSE vector A TRUE/FALSE vector the same length as the number of datasets, with exactly one TRUE corresponding to the selected data set.

See Also

Other option parsers: get_taxmap_cols(), get_taxmap_other_cols(), get_taxmap_table(), verify_taxmap()

Examples

## Not run: 
# Parse data
x = parse_tax_data(hmp_otus, class_cols = "lineage", class_sep = ";",
                   class_key = c(tax_rank = "taxon_rank", tax_name = "taxon_name"),
                   class_regex = "^(.+)__(.+)$")
                   
# Get data set by name
print(metacoder:::get_taxmap_table(x, "tax_data"))
print(metacoder:::get_taxmap_table(x, "invalid"))

# Get data set by index
print(metacoder:::get_taxmap_table(x, 1))
print(metacoder:::get_taxmap_table(x, 3)) # invalid

# Get data set by T/F vector
print(metacoder:::get_taxmap_table(x, c(T, F)))
print(metacoder:::get_taxmap_table(x, c(T, T))) # invalid
print(metacoder:::get_taxmap_table(x, c(T, F, F))) # invalid
                   

## End(Not run)

grunwaldlab/metacoder documentation built on Feb. 22, 2024, 3:47 a.m.