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 1.10.0 Index]