plotbeta: plot beta diversity

In guokai8/microbial: Do 16s Data Analysis and Generate Figures

plot beta diversity

Description

plot beta diversity

Usage

plotbeta(
  physeq,
  group,
  shape = NULL,
  distance = "bray",
  method = "PCoA",
  color = NULL,
  size = 3,
  ellipse = FALSE
)

Arguments

physeq	A phyloseq object containing merged information of abundance, taxonomic assignment, sample data including the measured variables and categorical information of the samples, and / or phylogenetic tree if available.
group	(Required). Character string specifying name of a categorical variable that is preferred for grouping the information. information.
shape	shape(Optional) Character string specifying shape of a categorical variable
distance	A string character specifying dissimilarity index to be used in calculating pairwise distances (Default index is "bray".). "unifrac","wunifrac","manhattan", "euclidean", "canberra", "bray", "kulczynski", "jaccard", "gower", "altGower", "morisita", "horn", "mountford", "raup" , "binomial", "chao", "cao" or "mahalanobis".
method	A character string specifying ordination method. All methods available to the ordinate function of phyloseq are acceptable here as well.
color	user defined color for group
size	the point size
ellipse	draw ellipse or not

Value

ggplot2 object

Author(s)

Kai Guo

Examples

{
data("Physeq")
phy<-normalize(physeq)
plotbeta(phy,group="SampleType")
}

guokai8/microbial documentation built on Oct. 15, 2024, 11:32 p.m.