amp_rabund: Generates a ggplot2 style rank abundance plot of the most...
In MadsAlbertsen/ampvis: Tools for visualising amplicon data

A nice long description

1	amp_rabund(data)

`data`	(required) A phyloseq object.
`group`	Group the data based on a sample variable.
`order.group`	A vector defining the order of groups.
`tax.show`	The number of taxa to show or a vector of taxa names (default: 50).
`scale.seq`	The number of sequences in the pre-filtered samples (default: 100)
`tax.clean`	Replace the phylum Proteobacteria with the respective Classes instead (default: T).
`plot.type`	Either "point", "boxplot" or "curve" (default: "boxplot").
`plot.log`	Log10 scale the data (default: F)
`output`	Either "plot" or "complete" (default: "plot").
`tax.add`	Additional taxonomic levels to display for each entry (default: "Phylum")
`tax.aggregate`	The taxonomic level that the data should be aggregated to (defualt: "Genus")
`tax.empty`	Either "remove" OTUs without taxonomic information, "rename" with best classification or add the "OTU" name (default: rename).
`tax.class`	Converts a specific phyla to class level instead (e.g. "p__Proteobacteria").
`point.size`	Size of points (default: 2).
`plot.flip`	Flip the axis of the plot (default: F).
`sort.by`	Sort the boxplot by either "median", "mean" or "total" (default = "median")
`adjust.zero`	Keep 0 abundances in ggplot2 median calculations by adding a small constant to these.
`plot.theme`	Chose different standard layouts choose from "normal" or "clean" (default: "normal").
`order.y`	A vector to order the y-axis by.