dimred_pcoa: Dimensionality reduction through PCoA
In animalcules: Interactive microbiome analysis toolkit

Description Usage Arguments Value Examples

Dimensionality reduction through PCoA

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

`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")

A list with a plotly object and summary table

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