Add full taxonomy path to a Kraken report data frame

This function requires that rows are in the order of the original Kraken report, so cannot be used after kraken_complete().

Usage

kraken_add_taxonomy(x)

Arguments

x

A data frame containing the fields "rank_code", "scientific_name", and "rank_level" with rows in the original order of the Kraken sample report(s), as returned by read_kraken_reports().

Details

You can apply this function to a data frame of Kraken reports for multiple samples; however, doing so is typically inefficient due to needing to recompute paths for taxa that appear in multiple samples. Instead, consider generating taxonomy paths from the original database and joining these to the kraken report data frame.