Man pages for MadsAlbertsen/ampvis2
Tools for visualising amplicon data
| AalborgWWTPs | A subset of the MiDAS example data |
| abundAreCounts | Check whether abundances appear to be read counts (i.e. not... |
| aggregate_abund | Aggregate OTUs to a specific taxonomic level |
| 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_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_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_rarecurve | Rarefaction curve |
| amp_rarefy | Rarefy ampvis2 object |
| amp_rename | Tidy up taxonomy |
| amp_timeseries | Abundance timeseries |
| amp_venn | Venn diagram of core OTUs |
| ampvis2 | 'ampvis2' package |
| as.data.table.DNAbin | Coerce DNAbin object to data.table |
| checkReqPkg | Check for installed package |
| dist.JSD | Calculate Jensen-Shannon Divergence distances |
| dist.unifrac | Calculate weighted or unweighted UniFrac distances. Adopted... |
| dot-onAttach | .onAttach |
| 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... |
| filter_otus | Filter OTUs by a threshold in percent |
| findOTUcol | Detect OTU/ASV column in a data frame |
| getLowestTaxLvl | Find lowest taxonomic level |
| getMiDASFGData | Get data from the MiDAS field guide API |
| import | Import any file format |
| is_ampvis2 | Check if data has class "ampvis2" |
| 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... |
| parseTaxonomy | Extract/parse taxonomy from a data.frame |
| pipe | Pipe operator |
| print.ampvis2 | Prints ampvis2 object summary (internal function) |
| print.coreplot | Prints amp_core plots if margin plots are also generated... |
| print.figcaption | Print method for figure caption created by amp_ordinate |
| print.hmfunplot | Prints heatmap+functions plot (internal function) |
| tax_levels | Valid taxonomic levels |
| unzip_file | Unzip file |
