ordination-sorting-taxa: Order taxa in phyloseq by their loading vectors

In david-barnett/microViz: Microbiome Data Analysis and Visualization

Order taxa in phyloseq by their loading vectors

Description

tax_sort_ord reorders taxa in a phyloseq object based on the relative length of their taxa scores / "loading" vector lengths on 1 or 2 ordination axes.

ord_order_taxa gets the taxa names in order from the ordination contained in a psExtra object. This is used internally by tax_sort_ord.

Usage

tax_sort_ord(ps, ord, axes = 1:2, scaling = 2)

ord_order_taxa(ord, axes = 1:2, scaling = 2)

Arguments

ps	phyloseq object to be sorted
ord	psExtra with ordination object
axes	which axes to use for sorting? numerical vector of length 1 or 2
scaling	Type 2, or type 1 scaling. For more info, see https://sites.google.com/site/mb3gustame/constrained-analyses/redundancy-analysis. Either "species" or "site" scores are scaled by (proportional) eigenvalues, and the other set of scores is left unscaled (from ?vegan::scores.cca)

See Also

• These functions were created to support ordering of taxa bars on ord_plot_iris

• ps_sort_ord for ordering samples in phyloseq by ordination

david-barnett/microViz documentation built on April 17, 2025, 4:25 a.m.