cipphyloseq: Adds Additional Features (plots, DESeq2) to phyloseq

Make a scatter PCA/PCOA plot of phyloseq object with complete biom and subset of samples – useful for conserved axes

pcoa_subset_biom(biom, method = "PCoA", distance = "unifrac", samples,
  color_category = NULL, shape_category = NULL, weighted = FALSE,
  title = NULL, colors = NULL, shapes = NULL, seed = 100,
  xrange = NULL, yrange = NULL)

`biom`	phyloseq object
`method`	data reduction method to use (default PCoA; see phyloseq ordinate)
`distance`	distance measure to use (default unifrac)
`samples`	samples to include on plot
`color_category`	variable in sample data (if any) to color points by
`shape_category`	variable in sample data (if any) to distinguish points by symbol
`weighted`	use weighted distance (normally only useful for unifrac)
`title`	title of plot
`shapes`	vector of shapes to use if you don't like the defaults
`seed`	random number generator seed (default 100)
`xrange`	optional range of acceptable points to plot in terms of x values
`yrange`	optional range of acceptable points to plot in terms of y values
`color`	vector of colors to use if you don't like the defaults