prop_tax_tab: Propagate taxon information down an entire 'tax_table' object

In JCSzamosi/aftersl1p: Generate Summary Graphics and Basic Analysis of 16s Data

Propagate taxon information down an entire tax_table object

Description

prop_tax_tab Takes the taxon assignment from the lowest assigned level in an OTU's assignment and fills it in to all the lower, unresolved fields.

Usage

prop_tax_tab(taxtab, indic)

Arguments

taxtab	a tax_table object
indic	a flag to indicate if the taxon names have level indicators. If FALSE, they are added. Just gets passed to prop_tax_row().

Details

Often taxon cannot be assigned all the way down to genus from the limited information available from a given variable region of 16S (or other marker gene). If an OTU has been assigned to Order Enterobacteriales, but the Family and genus cannot be resolved, then the Family and Genus fields are left blank by QIIME. This function fills those fields with the string 'o_Enterobacteriales', so they are not parsed as NAs by ggplot and other functions.

Value

A tax_table object with NAs replaced with higher-level taxon assignment

JCSzamosi/aftersl1p documentation built on July 3, 2025, 8:37 p.m.