reduce_names: Shorten taxonomic assignment in table row names

In OTUtable: North Temperate Lakes - Microbial Observatory 16S Time Series Data and Functions

Description

Reduces the full string indicating taxonomy to the last classified level. Works on tables at levels higher than OTUs.

Usage

reduce_names(table)

Arguments

table

A table containing the relative abundances of each taxa produced by combine_otus()

Value

Returns the same table with shortened row names

Note

This function is often most useful for plotting, so that the full string does not appear on the plot

Author(s)

Alexandra Linz <[e-mail]>

Examples

data(otu_table)
data(taxonomy)

# Create a small table for the example
# example <- year_subset("05", otu_table)
# example <- bog_subset("TBE", example)

# clade_table <- combine_otus("Clade", example, taxonomy)
# clade_table <- clade_table[which(rowSums(clade_table) > 0),]
# head(rownames(clade_table))
# reduced_clades <- reduce_names(clade_table)
# head(rownames(reduced_clades))

Example output

OTUtable documentation built on May 1, 2019, 10:51 p.m.