NMDSplot

This function generates a Non-metric Multidimensional Scaling (NMDS) 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

NMDSplot(
  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 outdir for the output files

width

The width of the output NMDS plot (default: 6)

height

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

color

A vector of colors for the groups in the plot

save_output

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

Value

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

Examples

if (FALSE) {
beta_diversity <- GetBetaDiversity(mmo, method = 'Gen.Uni',
 normalization = 'None', distance = 'dreams', filter_id = FALSE)
# Use method = 'bray' or 'jaccard' if you want to use just feature abundance
# without considering feature spectral dissimilarity
NMDSplot(mmo, betadiv = beta_diversity, outdir = 'output/NMDS', width = 6, height = 6)
}