Tools for visualising amplicon data

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Documentation for package ‘ampvis2’ version 2.8.9

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_otus Filter OTUs by a threshold in percent
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 Functional information about microbes at Genus level
normaliseTo100 Normalise read counts to 100, i.e. in percent relative abundance per sample