beta_ordination: Plot beta ordination function

In ericjcgalvez/MicrobiomeWrangler:

Plot beta ordination function

Description

This function performs ordination plots and adonis test

Usage

beta_ordination(
  phylo,
  formula = "",
  color,
  distance_method = "bray",
  ordination_type = "NMDS",
  geom_star = TRUE,
  permutations = 999,
  parallel = 4,
  shape = NULL,
  tagtype = "A",
  verbose = TRUE,
  layout = c(area(1, 1), area(2, 1, 5))
)

Arguments

phylo	Phyloseq object
formula	stats for adonis i.e. c("Genotype + Experiment + Cage.ID")
color	metadata category color
distance_method	Similarity or distance measurement i.e. "bray", "jaccard", "uunifrac", "wunifrac"
ordination_type	Type of ordination that should be performed
geom_star	boolean. If TRUE create a star plot by drawing segments from group centroid to each points.
permutations	a list of control values for the permutations as returned by the function how, or the number of permutations required, or a permutation matrix where each row gives the permuted indices.
parallel	Parallel computations
shape	metadata category shape
tagtype	Label type of the plots. i.e. "A" "1" "I".
verbose	If TRUE calculation results will be printed. If FALSE not.
layout	List of patch_area objects. Control the plot layout.

Examples

data("mice_B6_N")
beta_ordination(mice_B6_N, mycolor = "Genotype", myshape = "Experiment",
myformula = c("Genotype + Experiment + Cage.ID"))

ericjcgalvez/MicrobiomeWrangler documentation built on April 14, 2022, 6:33 p.m.