pcoa_biom: Make a scatter PCA/PCOA plot of phyloseq object

In jhbadger/cipphyloseq: Adds Additional Features (plots, DESeq2) to phyloseq

Description

Make a scatter PCA/PCOA plot of phyloseq object

Usage

pcoa_biom(biom, method = "PCoA", distance = "unifrac",
  color_category = NULL, shape_category = NULL, weighted = FALSE,
  title = NULL, colors = NULL, shapes = NULL,
  label_category = NULL, order_category = NULL, permanova = FALSE,
  point_size = 1)

Arguments

biom	phyloseq object
method	data reduction method to use (default PCoA; see phyloseq ordinate)
distance	distance measure to use (default unifrac)
color_category	variable in sample data (if any) to color points by
shape_category	variable in sample data (if any) to distinguish points by symbol
weighted	use weighted distance (normally only useful for unifrac)
title	title of plot
shapes	vector of shapes to use if you don't like the defaults
label_category	variable in sample data (if any) to label points
permanova	– include PERMANOVA analysis on color_category
point_size	size of points on graph
color	vector of colors to use if you don't like the defaults

Examples

pcoa_biom()

jhbadger/cipphyloseq documentation built on May 24, 2019, 2:04 a.m.