Tools for visualising amplicon data

Documentation for package ‘ampvis’ version 1.27.0

ampvis-package	ampvis: amplicon visualisation
ampvis	ampvis: amplicon visualisation
amp_cleanMiF	Make raw MiDAS function data into ampvis format
amp_core	Generates a ggplot2 style core community plots
amp_correlation	Generates correlation networks from amplicon data.
amp_export	Export sequences from a phyloseq object
amp_export_table	Export otutable from a phyloseq object
amp_function	Generate a function table
amp_heatmap	Generate a heatmap from amplicon data
amp_load	Load data as OTU table and convert to a phyloseq object.
amp_ordinate	Generates a ggplot2 style ordinate plot of amplicon data.
amp_rabund	Generates a ggplot2 style rank abundance plot of the most abundant OTUs
amp_rarecurve	Calculate rarefaction curve for each sample.
amp_rename	Used for cleaning and renaming taxonomy in phyloseq objects
amp_stability	Calculate similarity over time
amp_stats	Calculate basic statistics for each sample
amp_test_cluster	Tests if there is a significant difference between samples.
amp_test_species	Tests if there is a significant difference in abundance between selected conditions
amp_venn	Generates a ggplot2 style venn diagram
data	Tests if there is a significant difference in abundance between selected conditions