envtoverlay: Environmental variable fitting to unconstrained ordination...

In sw1/theseus: Analysis and Visualization Tools for Microbial Community Data

Description

Fits environmental variables as vectors (via envfit) and smooth surfaces (via ordisurf) to an ordination diagram. The figure is faceted if multiple variables are specified.

Usage

envtoverlay(PS, covariates, ordmet = "PCA")

Arguments

PS	(required) A phyloseq object.
covariates	(required) A character vector of covariates present in the phyloseq objects sample_data().
ordmet	Ordination method. Options are Principal Component Analysis ("PCA") or Correspondence Analysis ("CA"). Defaults to "PCA".

Value

A ggplot object.

See Also

rda cca envfit ordisurf

Examples

## Not run: 
library(theseus)
library(phyloseq)
library(ggplot2)
data('WWTP_Impact')
cv <- c('log_NO3N', 'log_PO4')
p.eo <- envtoverlay(WWTP_Impact, covariates=cv)
p.eo

## End(Not run)

sw1/theseus documentation built on May 4, 2019, 4:22 p.m.