amp_test_species: Tests if there is a significant difference in abundance...
In MadsAlbertsen/ampvis: Tools for visualising amplicon data

A nice long description

1	amp_test_species(data, design)

`data`	(required) A phyloseq object including sample data.
`group`	(required) The group to test against.
`tax.aggregate`	Group data at specific taxonomic level (default: "OTU").
`sig`	Significance treshold (default: 0.01).
`fold`	Log2fold filter default for displaying significant results (default: 0)
`tax.class`	Converts a specific phyla to class level instead (e.g. "p__Proteobacteria").
`tax.empty`	Either "remove" OTUs without taxonomic information at X level, with "best" classification or add the "OTU" name (default: best).
`label`	Label the significant entries with tax.display (default:F).
`plot.type`	Either "boxplot" or "point" (default: point)
`plot.show`	Display the X most significant results.
`plot.point.size`	The size of the plotted points.
`plot.theme`	Chose different standard layouts choose from "normal" or "clean" (default: "normal").
`parallel`	To run DESeq2 in parallel mode (default: F)
`adjust.zero`	Keep 0 abundances in ggplot2 median calculations by adding a small constant to these.
`tax.display`	Display additional taxonomic levels in the plot output e.g. "Genus".