PCoAplot — PCoAplot • ecomet

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, prefix, width = 6, height = 6, color)

Arguments

mmo: The mmo object containing metadata
betadiv: The beta diversity distance matrix, output of GetBetaDiversity
prefix: 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

Examples

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