Tools for visualising amplicon data

Documentation for package ‘ampvis2’ version 2.7.24

AalborgWWTPs	A subset of the MiDAS example data
amp_alphadiv	Alpha-diversity analysis
amp_alpha_diversity	Alpha-diversity analysis
amp_boxplot	Boxplot
amp_core	Grouped core community analysis
amp_export_fasta	Export raw DNA sequences
amp_export_long	Transform ampvis2 objects into a long-format data frame
amp_export_otutable	Export OTU-table
amp_filter_samples	Subset ampvis2 objects based on sample metadata
amp_filter_taxa	Subset ampvis2 objects based on taxonomy
amp_frequency	Frequency plot
amp_heatmap	Heatmap
amp_import_biom	(Defunct) Import OTU table from BIOM file
amp_import_usearch	(Defunct) Import OTU table from USEARCH pipelines
amp_load	Load data for ampvis2 functions
amp_mergereplicates	Merge replicate samples
amp_merge_ampvis2	Merge ampvis2 object(s)
amp_merge_replicates	Merge replicate samples
amp_octave	Octave plot
amp_ordinate	Ordination plot
amp_otu_network	Network plot
amp_rankabundance	Rank abundance plot
amp_rank_abundance	Rank abundance plot
amp_rarecurve	Rarefaction curve
amp_rarefaction_curve	Rarefaction curve
amp_subset_samples	Subset ampvis2 objects based on sample metadata
amp_subset_taxa	Subset ampvis2 objects based on taxonomy
amp_timeseries	Abundance timeseries
amp_time_series	Abundance timeseries
amp_venn	Venn diagram of core OTUs
example_metadata	A minimal example of sample metadata
example_otutable	A minimal example of an OTU-table
example_taxonomy	A minimal example of taxonomy
MiDAS	MiDAS example data
midasfunctions_20201201	Functional information about microbes at Genus level