Reference

Data and filtering Functions for loading, exporting and subsetting the data.
amp_load()	Load data for ampvis2 functions
amp_filter_samples() amp_subset_samples()	Subset ampvis2 objects based on sample metadata
amp_filter_taxa() amp_subset_taxa()	Subset ampvis2 objects based on taxonomy
amp_merge_replicates() amp_mergereplicates()	Merge replicate samples
amp_merge_ampvis2()	Merge ampvis2 object(s)
amp_import_biom()	(Defunct) Import OTU table from BIOM file
amp_import_usearch()	(Defunct) Import OTU table from USEARCH pipelines
amp_export_fasta()	Export raw DNA sequences
amp_export_otutable()	Export OTU-table
amp_export_long()	Transform ampvis2 objects into a long-format data frame
Summary functions
amp_alphadiv() amp_alpha_diversity()	Alpha-diversity analysis
Plotting functions Functions for visualising amplicon data.
amp_rarecurve() amp_rarefaction_curve()	Rarefaction curve
amp_octave()	Octave plot
amp_boxplot()	Boxplot
amp_heatmap()	Heatmap
amp_ordinate()	Ordination plot
amp_timeseries() amp_time_series()	Abundance timeseries
amp_venn()	Venn diagram of core OTUs
amp_core()	Grouped core community analysis
amp_frequency()	Frequency plot
amp_otu_network()	Network plot
amp_rankabundance() amp_rank_abundance()	Rank abundance plot
Utility functions Various utility functions that are also used internally in several ampvis2 functions, but may also be useful in other custom scenarios.
amp_rarefy()	Rarefy ampvis2 object
normaliseTo100()	Normalise read counts to 100, i.e. in percent relative abundance per sample
filter_otus() filter_species()	Filter OTUs by a threshold in percent
aggregate_abund()	Aggregate OTUs to a specific taxonomic level
matchOTUs()	Rename OTUs by exact sequence matches from a FASTA file
Data sets
MiDAS	MiDAS example data
AalborgWWTPs	A subset of the MiDAS example data
example_metadata	A minimal example of sample metadata
example_otutable	A minimal example of an OTU-table
example_taxonomy	A minimal example of taxonomy
midasfunctions	Functional information about microbes at Genus level