Data and filtering

Functions for loading, exporting and subsetting the data.

amp_load

Load data for ampvis functions

amp_subset_samples

Subset ampvis2 objects based on sample metadata

amp_subset_taxa

Subset ampvis2 objects based on taxonomy

amp_import_biom

Import OTU table from BIOM file

amp_import_usearch

Import OTU table from USEARCH pipelines

amp_export_fasta

Export raw DNA sequences

amp_export_otutable

Export OTU-table

Plotting functions

Functions for visualising amplicon data.

amp_rarecurve

Rarefaction curve

amp_boxplot

Boxplot

amp_heatmap

Heatmap

amp_ordinate

Ordination plot

amp_core

Core community analysis

amp_timeseries

Abundance timeseries

amp_otu_network

Network plot

amp_frequency

Frequency plot

amp_rankabundance

Rank abundance plot

amp_alphadiv

Alpha-diversity analysis

amp_venn

Venn diagram of core OTUs