amp_core: Generates a ggplot2 style core community plots

In MadsAlbertsen/ampvis: Tools for visualising amplicon data

Description

A nice long description

Usage

amp_core(data)

Arguments

data	(required) A phyloseq object (or a list).
group	Group the data based on a sample variable (default: "Sample").
scale.seq	The number of sequences in the pre-filtered samples (default: 100)
tax.class	Converts a specific phyla to class level instead (e.g. "p__Proteobacteria").
tax.empty	Either "remove" OTUs without taxonomic information, add "best" classification or add the "OTU" name (default: best).
plot.type	Either core or frequency (default: frequency).
output	Either plot or complete (default: "plot").
tax.aggregate	The taxonomic level that the data should be aggregated to (default: OTU).
weight	Weight the frequency by abundance (default: T).
abund.treshold	Treshold for considering something abundant in percent (default: 0.1).

Value

A ggplot2 object

Author(s)

Mads Albertsen [e-mail]

MadsAlbertsen/ampvis documentation built on May 7, 2019, 2:08 p.m.