# Tools for visualising amplicon data

## Documentation for package ‘ampvis’ version 1.27.0

- DESCRIPTION file.

## Help Pages

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