# Tools for visualising amplicon data

## Documentation for package ‘ampvis2’ version 2.7.12

- DESCRIPTION file.

## Help Pages

.onAttach | .onAttach
AalborgWWTPs | A subset of the MiDAS example data
aggregate_abund | Aggregate OTUs to a specific taxonomic level
ampvis2 | 'ampvis2' package
amp_alphadiv | 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_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_octave | Octave plot
amp_ordinate | Ordination plot
amp_otu_network | Network plot
amp_rankabundance | Rank abundance plot
amp_rarecurve | Rarefaction curve
amp_rarefy | Rarefy ampvis2 object
amp_rename | Tidy up taxonomy
amp_subset_samples | Subset ampvis2 objects based on sample metadata
amp_subset_taxa | Subset ampvis2 objects based on taxonomy
amp_timeseries | Abundance timeseries
amp_venn | Venn diagram of core OTUs
checkReqPkg | Check for installed package
dist.JSD | Calculate Jensen-Shannon Divergence distances
example_metadata | A minimal example of sample metadata
example_otutable | A minimal example of an OTU-table
example_taxonomy | A minimal example of taxonomy
extractFunctions | Extract functional information about Genera from the MiDAS field guide
filter_species | Filter species by a threshold in percent
getLowestTaxLvl | Find lowest taxonomic level
getMiDASFGData | Get data from the MiDAS field guide API
is_ampvis2 | Check if data has class "ampvis2"
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
print.ampvis2 | Prints ampvis2 object summary (internal function)
print.coreplot | Prints amp_core plots if margin plots are also generated (internal function)
print.figcaption | Print method for figure caption created by amp_ordinate
print.hmfunplot | Prints heatmap+functions plot (internal function)
unifrac | Calculate weighted or unweighted UniFrac distances. Adopted from fastUniFrac() from phyloseq