dimred_pcoa {animalcules}R Documentation

Dimensionality reduction through PCoA

Description

Dimensionality reduction through PCoA

Usage

dimred_pcoa(MAE, tax_level, color, shape = NULL, axx = 1, axy = 2,
  axz = NULL, method = c("bray", "jaccard"))

Arguments

MAE

A multi-assay experiment object

tax_level

The taxon level used for organisms

color

A condition to color data points by e.g. "AGE"

shape

A condition to shape data points by e.g. "SEX"

axx

Principle coordinate on the x-axis e.g. 1

axy

Principle coordinate on the y-axis e.g. 2

axz

Principle coordinate on the z-axis e.g. 2

method

Method to use e.g. c("bray", "jaccard")

Value

A list with a plotly object and summary table

Examples

data_dir = system.file("extdata/MAE.rds", package = "animalcules")
toy_data <- readRDS(data_dir)
result <- dimred_pcoa(toy_data,
                      tax_level="genus",
                      color="AGE",
                      shape="DISEASE",
                      axx=1,
                      axy=2,
                      method="bray")
result$plot
result$table


[Package animalcules version 1.0.5 Index]