# Tools for visualising amplicon data

## Documentation for package ‘ampvis2’ version 2.7.27

- DESCRIPTION file.

## Help Pages

AalborgWWTPs | A subset of the MiDAS example data
aggregate_abund | Aggregate OTUs to a specific taxonomic level
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_rarefy | Rarefy ampvis2 object
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
filter_species | Filter OTUs by a threshold in percent
matchOTUs | Rename OTUs by exact sequence matches from a FASTA file
MiDAS | MiDAS example data
midasfunctions_20201201 | Functional information about microbes at Genus level
normaliseTo100 | Normalise read counts to 100, i.e. in percent relative abundance per sample