PCoA3D: PCoA3D

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 plotly's 3d plotting.

Usage

PCoA(METRIC="braycurtis", METADATA=experiment_metadata, FEATURES=otutable, TREE=ggtree, COLOR="Time", SHAPE="Group", SUBSAMPLE=TRUE, AXIS=c(1,2,3), PALETTE=c("red","green"))

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 or shape points by where sample is row name.
FEATURES	Table of feature counts where Samples are columns, and IDs are row names.
TREE	A phylogenetic tree of phylo class *only required for UniFrac Metrics
COLOR	Metadata column to color samples by. Defaults to none.
SHAPE	Metadata column to shape samples by. Defaults to none.
SUBSAMPLE	Should table be subsampled? TRUE/FALSE (default: TRUE)
AXIS	Which PCs should be plotted? Expects a numeric vector of length 3. defaults to AXIS=c(1,2,3)
PALETTE	a vector of COLORS to be used? defaults to the rainbow palette.

Value

Returns plot.

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