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_timeseries()

Abundance timeseries

amp_venn()

Venn diagram of core OTUs

amp_core()

Core community analysis

amp_frequency()

Frequency plot

amp_otu_network()

Network plot

amp_rankabundance()

Rank abundance plot

amp_alphadiv()

Alpha-diversity analysis