Man pages for SWittouck/tidyamplicons
Functions to Manipulate and Visualize Amplicon Abundance Data
| abundances | Extract the abundance table |
| abundances_matrix | Return an abundances matrix |
| add_alphas | Add alpha diversity measures |
| add_cluster | Add cluster number |
| add_codifab | Perform compositional differential abundance analysis |
| add_copca | Add compositional principal components to the sample table |
| add_diversity_measures | Add some alpha diversity measures |
| add_jervis_bardy | Apply the taxon QC method of Jervis-Bardy |
| add_lib_size | Add total abundance per sample |
| add_logratios | Add logratios |
| add_max_rel_abundance | Add the maximum relative abundance of taxa to the taxon table |
| add_mean_rel_abundances | Add average relative abundances |
| add_occurrences | Add taxon occurrences to the taxon table |
| add_pcoa | Add first two dimensions of PCOA |
| add_presence_counts | Add absolute occurrences of taxa to the taxon table |
| add_rel_abundance | Add relative abundance to abundance table |
| add_rel_occurrence | Add the relative occurrence of taxa to the taxon table |
| add_sample_clustered | Add clustered sample order |
| add_sample_tibble | Add sample table to the tidyamplicons object |
| add_spike_ratio | Add spike ratio |
| add_taxon_name | Create sensible names for the taxa and add to taxon table |
| add_taxon_name_color | Create taxon names suitable for visualization with color. A... |
| add_taxon_tibble | Add taxon metadata to the tidyamplicons object |
| add_total_rel_abundance | Add the total relative abundance of taxa to the taxon table |
| aggregate_samples | Aggregate samples with identical values for all metadata |
| aggregate_taxa | Aggregate taxa on a given taxonomic rank |
| as_abundances | Convert matrix with abundances to tidy data frame |
| as_abundances_matrix | Convert abundances tidy data frame to matrix. |
| as_phyloseq | Convert tidyamplicons object to phyloseq object |
| as_tidyamplicons | Convert phyloseq object to tidyamplicons object |
| bar_plot | Return a bar plot of the samples |
| bar_plot_ly | Return an interactive bar plot of the samples |
| betas | Get beta diversity table |
| change_id_samples | Change sample IDs to a given expression |
| change_id_taxa | Change taxon IDs to a given expression |
| classify_taxa | (Re)classify amplicon sequences |
| codifab_plot | Generate a compositional differential abundance plot |
| create_test_ta | Create a tidyamplicons object for testing/example purporses |
| create_tidyamplicons | Initiate tidyamplicons object |
| everything | Get all data in one single table |
| filter_abundances | Filter the abundances |
| filter_samples | Filter the samples |
| filter_taxa | Filter the taxa |
| get_abundances_extended | Synonym of 'everything'. |
| get_bar_plot | Return a bar plot of the samples |
| get_betas | Get beta diversity table |
| get_history_plot | Return a history plot of the samples |
| get_numbers | Return some descriptive numbers |
| get_rel_abundance_matrix | Return a relative abundance matrix |
| history_plot | Return a history plot of the samples |
| make_tidyamplicons | Create a tidyamplicons object from three tidy tables |
| mean_rel_abundances | Get mean relative abundances of taxa in general or per... |
| merge_samples | Synonym of 'aggregate_samples'. |
| merge_taxa | Synonym of 'aggregate_taxa'. |
| merge_tidyamplicons | Merge two tidyamplicons objects. |
| mutate_abundances | Create extra variables in the abundances table |
| mutate_samples | Create extra variables in the sample table |
| mutate_taxa | Create extra variables in the taxon table |
| numbers | Return some descriptive numbers |
| occurrences | Get occurrences of taxa in general or per condition |
| pcoa_plot_ly | Return an interactive pcoa plot of the samples |
| perform_adonis | Perform an adonis test |
| pipe | Pipe operator |
| process_abundance_selection | Apply an abundance filtering to the taxon table |
| process_sample_selection | Apply a sample filtering to the taxon and abundance tables |
| process_taxon_selection | Apply a taxon filtering to the abundance table |
| rank_names | Return rank names associated with a tidyamplicons object |
| rarefy | Rarefy the samples to a given number of reads |
| read_tidyamplicons | Read community data written by tidyamplicons |
| remove_empty_samples | Removes empty samples from the tidyamplicons object |
| report_numbers | Report numbers |
| reset_ids | Reset the taxon and sample IDs |
| sample_plot | Return a visualization designed for a small number of samples |
| samples | Extract the sample table |
| select_abundances | Retain or remove a set of abundance variables |
| select_samples | Retain or remove a set of sample variables |
| select_taxa | Retain or remove a set of taxon variables |
| set_rank_names | Set rank names for a tidyamplicons object |
| taxa | Extract the taxon table |
| taxon_counts_in_conditions | Get occurrences of taxa in general or in conditions |
| tidyamplicons | tidyamplicons: Functions to manipulate and visualize amplicon... |
| tidyeval | Tidy eval helpers |
| tidy_phyloseq | Convert phyloseq object to tidyamplicons object |
| trim_asvs | Trim all sequences |
| update_id_names | Rename the "sample" and "taxon" columns to "sample_id" and... |
| update_lib_sizes | Update library sizes in the lib_size table |
| update_tidyamplicons | Update old tidyamplicons object to new one. |
| write_tidyamplicons | Write community data in tidyamplicons format |
