plot_ordination: Plot first several principle coordinates of ordination

In kimberlyroche/ROL: What the package does (short line)

Description

Plot first several principle coordinates of ordination

Usage

plot_ordination(
  tax_level = "ASV",
  which_measure = "Sigma",
  annotation = "host",
  MAP = FALSE,
  spike_in = FALSE,
  show_plot = FALSE
)

Arguments

tax_level	taxonomic level at which to agglomerate data
which_measure	estimated object to visualize, either Lambda or Sigma
annotation	label to assign (e.g. individual)
MAP	use MAP estimate model output instead of full posterior output
spike_in	copy and permute the samples and calculate distances to these too, so as to give upper bound on distances
show_plot	show() plot of first 2 principle coordinates (in addition to rendering first 4 PCoA to files)

Examples

plot_ordination(tax_level="ASV", which_measure="Sigma", annotation="host", MAP=FALSE)

kimberlyroche/ROL documentation built on Dec. 10, 2020, 2:18 a.m.