PCoAplot

This function generates a Principal Coordinates Analysis (PCoA) plot based on the provided beta diversity distance matrix. It also performs PERMANOVA analysis to assess the significance of group differences and saves the results to CSV files.

Usage

PCoAplot(
  mmo,
  betadiv,
  outdir,
  width = 6,
  height = 6,
  color = NULL,
  save_output = TRUE
)

Arguments

mmo

The mmo object containing metadata

betadiv

The beta diversity distance matrix, output of GetBetaDiversity

outdir

The prefix for the output files

width

The width of the output PCoA plot (default: 6

height

The height of the output PCoA plot (default: 6)

color

A vector of colors for the points in the plot

save_output

A logical value indicating whether to save the output plot (default: TRUE)

Value

A list containing the PCoA plot, the PCoA coordinates, and the PERMANOVA results

Examples

if (FALSE) {
beta_diversity <- GetBetaDiversity(mmo, method = 'Gen.Uni',
 normalization = 'None', distance = 'dreams', filter_id = FALSE)
PCoAplot(mmo, betadiv = beta_diversity, outdir = 'output/PCoA', width = 6, height = 6)
}