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_mergereplicates()
Merge replicate samples
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
amp_export_long()
Transform ampvis2 objects into a long-format data frame
Functions for visualising amplicon data.
amp_rarecurve()
Rarefaction curve
amp_octave()
Octave plot
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