Tools for visualising amplicon data

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Documentation for package ‘ampvis2’ version 2.7.17

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