prop_tax_down: Propagate taxon information down an entire 'tax_table' in a...

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

Propagate taxon information down an entire tax_table in a phylose object

Description

prop_tax_down 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_down(physeq, indic, dbig = TRUE)

Arguments

physeq	a phyloseq object with a filled tax_table slot.
indic	a flag to indicate if the taxon names have level indicators. If FALSE, they are added. Just gets passed to prop_tax_tab().
dbig	a flag to indicate whether genus names that exist in multiple families should be disambiguated by appending the family name.

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 phyloseq object whose tax_table has had NAs replaced with the higher level taxon assignments.

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