plot_axes: Plot a pair of principal coordinates
In kimberlyroche/ROL: What the package does (short line)

Description Usage Arguments Details Examples

Plot a pair of principal coordinates

plot_axes(
  coordinates = NULL,
  centroids,
  tax_level = "ASV",
  axis1 = 1,
  axis2 = 2,
  annotation = "host",
  MAP = FALSE,
  show_plot = FALSE
)

`coordinates`	data.frame of coordinates from posterior embedding
`centroids`	data.frame of centroids from posterior embedding
`tax_level`	taxonomic level at which to agglomerate data
`axis1`	PCoA coordinate to display on x-axis
`axis2`	PCoA coordinate to display on y-axis
`annotation`	label to assign (e.g. individual)
`MAP`	use MAP estimate model output instead of full posterior output
`show_plot`	show() plot in addition to rendering it to a file

Coordinates parameter is only necessary where we're plotting full host posteriors (i.e. where annotation="host").

tax_level <- "genus"
annotation <- "group"
MAP <- FALSE
centroids <- readRDS(file.path("output","plots",tax_level,"Sigma_ordination_centroids.rds"))
labelled_centroids <- get_other_labels(centroids=centroids, tax_level=tax_level, annotation=annotation, MAP=MAP)
plot_axes(coordinates=labelled_centroids, tax_level=tax_level, axis1=1, axis2=2, annotation=annotation, MAP=MAP)