PCoA: PCoA

In jbisanz/MicrobeR: Handy functions for microbiome analysis in R

Description

UniFrac is implimented as per Phyloseq, Bray Curtis from Vegan, Jensen-Shannon divergence from Phyloseq, and PCoA from APE. Plotting via ggplot2. Will also carry out ADONIS and return p and r2 in plot title. Distances calculated from proportions.

Usage

PCoA(METRIC="braycurtis", METADATA=experiment_metadata, FEATURES=otutable, TREE=ggtree, COLOR="Time", SHAPE="Group", SUBSAMPLE=TRUE, AXIS=c(1,2))

Arguments

METRIC	Desired beta-diversity metric, options are Bray Curtis (braycurtis), Weighted UniFrac (weightedunifrac), UnWeighted UniFrac (unweightedunifrac), Jensen-Shannon diversgence (jsd).
METADATA	Metadata Table with variables to color PCoAs by
FEATURES	Table of feature/OTU/SV counts where Samples are columns, and IDs are row names
TREE	Table of feature/OTU/SV counts where Samples are columns, and IDs are row names, only required for UniFrac Metrics
COLOR	Metadata column to color samples by. Defaults to sample names from metadata row names.
SHAPE	Metadata column to shape samples by. Defaults to none.
SUBSAMPLE	Should table be subsampled? TRUE/FALSE (default: TRUE)
AXIS	Which Axis should be plotted? Expects a numeric vector of length 2. defaults to Pco1 and Pco2 AXIS=c(1,2)
ADONIS	Should ADONIS test be applied ? TRUE/FALSE (default TRUE)

Value

Returns a ggplot

jbisanz/MicrobeR documentation built on June 5, 2019, 7:53 p.m.