API for metacoder
Tools for Parsing, Manipulating, and Graphing Taxonomic Abundance Data
| Global functions | |
|---|---|
| %>% | Man page |
| .onAttach | Man page Source code |
| DNAbin_to_char | Man page Source code |
| `%||%` | Source code |
| add_alpha | Man page Source code |
| add_names | Source code |
| all_empty | Source code |
| all_functions | Man page Source code |
| all_names | Man page Source code |
| all_names.Taxmap | Source code |
| all_names.Taxonomy | Source code |
| all_names.default | Source code |
| ambiguous_patterns | Man page Source code |
| ambiguous_synonyms | Man page Source code |
| apply_color_scale | Man page Source code |
| arrange_obs | Man page Source code |
| arrange_obs.Taxmap | Source code |
| arrange_obs.default | Source code |
| arrange_taxa | Man page Source code |
| arrange_taxa.Taxonomy | Source code |
| arrange_taxa.default | Source code |
| as_id | Man page Source code |
| as_phyloseq | Man page Source code |
| assert | Source code |
| branches | Man page Source code |
| branches.Taxonomy | Source code |
| branches.default | Source code |
| calc_diff_abund_deseq2 | Man page Source code |
| calc_group_mean | Man page Source code |
| calc_group_median | Man page Source code |
| calc_group_rsd | Man page Source code |
| calc_group_stat | Man page Source code |
| calc_n_samples | Man page Source code |
| calc_obs_props | Man page Source code |
| calc_prop_samples | Man page Source code |
| calc_taxon_abund | Man page Source code |
| can_be_num | Man page Source code |
| can_be_used_in_taxmap | Man page Source code |
| capitalize | Man page Source code |
| centroid | Source code |
| check_class_col | Man page Source code |
| check_element_length | Man page Source code |
| check_for_pkg | Man page Source code Source code |
| check_option_groups | Man page Source code |
| check_taxmap_data | Man page Source code |
| classifications | Man page Source code |
| classifications.Taxonomy | Source code |
| classifications.default | Source code |
| compare_groups | Man page Source code |
| complement | Man page Source code |
| contains | Man page |
| convert_base | Man page Source code Source code |
| correct_taxon_names | Man page Source code |
| count_capture_groups | Man page Source code |
| counts_to_presence | Man page Source code |
| csep2vec | Source code |
| ct | Source code |
| data_used | Man page |
| database_list | Man page |
| deg2rad | Source code |
| desc_font | Man page Source code |
| diverging_palette | Man page Source code |
| do_calc_on_num_cols | Man page Source code |
| edge_list_depth | Man page Source code |
| ends_with | Man page |
| error_font | Man page Source code |
| euclid | Source code |
| everything | Man page |
| ex_hierarchies | Man page |
| ex_hierarchy1 | Man page |
| ex_hierarchy2 | Man page |
| ex_hierarchy3 | Man page |
| ex_taxmap | Man page |
| extract_tax_data | Man page Source code |
| fasta_headers | Man page Source code |
| filter_ambiguous_taxa | Man page Source code |
| filter_obs | Man page Source code |
| filter_obs.Taxmap | Source code |
| filter_obs.default | Source code |
| filter_taxa | Man page Source code |
| filter_taxa.Taxmap | Source code |
| filter_taxa.Taxonomy | Source code |
| filter_taxa.default | Source code |
| filtering-helpers | Man page |
| get_class_from_el | Man page Source code |
| get_data | Man page Source code |
| get_data.Taxonomy | Source code |
| get_data.default | Source code |
| get_data_frame | Man page Source code |
| get_data_frame.Taxonomy | Source code |
| get_data_frame.default | Source code |
| get_database_name | Man page Source code |
| get_dataset | Man page Source code |
| get_dataset.Taxmap | Source code |
| get_dataset.default | Source code |
| get_dots_or_list | Man page Source code |
| get_edge_children | Man page Source code |
| get_edge_parents | Man page Source code |
| get_expected_data | Man page Source code |
| get_node_children | Man page Source code |
| get_numeric_cols | Man page Source code |
| get_numerics | Man page Source code |
| get_optimal_range | Man page Source code |
| get_sort_var | Man page Source code |
| get_taxmap_cols | Man page Source code |
| get_taxmap_data | Man page Source code |
| get_taxmap_other_cols | Man page Source code |
| get_taxmap_table | Man page Source code |
| get_taxonomy_levels | Man page Source code |
| heat_tree | Man page Source code |
| heat_tree.Taxmap | Man page Source code |
| heat_tree.default | Man page Source code |
| heat_tree_matrix | Man page Source code |
| helpers_fxn_se | Source code |
| hierarchies | Man page Source code |
| hierarchy | Man page Source code |
| highlight_taxon_ids | Man page Source code |
| hmp_otus | Man page |
| hmp_samples | Man page |
| id_classifications | Man page Source code |
| id_classifications.Taxonomy | Source code |
| id_classifications.default | Source code |
| ids | Man page Source code |
| init_taxmap_data | Man page Source code |
| inter_circle_gap | Man page Source code |
| internodes | Man page Source code |
| internodes.Taxonomy | Source code |
| internodes.default | Source code |
| intersect_line_rectangle | Source code |
| inverse | Man page |
| is_ambiguous | Man page Source code |
| is_branch | Man page Source code |
| is_branch.Taxonomy | Source code |
| is_branch.default | Source code |
| is_internode | Man page Source code |
| is_internode.Taxonomy | Source code |
| is_internode.default | Source code |
| is_leaf | Man page Source code |
| is_leaf.Taxonomy | Source code |
| is_leaf.default | Source code |
| is_root | Man page Source code |
| is_root.Taxonomy | Source code |
| is_root.default | Source code |
| is_stem | Man page Source code |
| is_stem.Taxonomy | Source code |
| is_stem.default | Source code |
| label_bounds | Man page Source code |
| layout_functions | Man page Source code |
| leaves | Man page Source code |
| leaves.Taxonomy | Source code |
| leaves.default | Source code |
| leaves_apply | Man page Source code |
| leaves_apply.Taxonomy | Source code |
| leaves_apply.default | Source code |
| length_of_thing | Man page Source code |
| limited_print | Man page Source code Source code |
| line_coords | Man page Source code |
| look_for_na | Man page Source code |
| lookup_tax_data | Man page Source code |
| make_dada2_asv_table | Man page Source code |
| make_dada2_tax_table | Man page Source code |
| make_fasta_with_u_replaced | Man page Source code |
| make_plot_legend | Man page Source code |
| map_data | Man page Source code |
| map_data.Taxonomy | Source code |
| map_data.default | Source code |
| map_data_ | Man page Source code |
| map_data_.Taxonomy | Source code |
| map_data_.default | Source code |
| map_unique | Man page Source code Source code |
| matches | Man page |
| metacoder | Man page |
| molten_dist | Man page Source code |
| multi_sep_split | Man page Source code |
| mutate_obs | Man page Source code |
| mutate_obs.Taxmap | Source code |
| mutate_obs.default | Source code |
| my_print | Man page Source code |
| n_leaves | Man page Source code |
| n_leaves.Taxonomy | Source code |
| n_leaves.default | Source code |
| n_leaves_1 | Man page Source code |
| n_leaves_1.Taxonomy | Source code |
| n_leaves_1.default | Source code |
| n_obs | Man page Source code |
| n_obs.Taxmap | Source code |
| n_obs.default | Source code |
| n_obs_1 | Man page Source code |
| n_obs_1.Taxmap | Source code |
| n_obs_1.default | Source code |
| n_subtaxa | Man page Source code |
| n_subtaxa.Taxonomy | Source code |
| n_subtaxa.default | Source code |
| n_subtaxa_1 | Man page Source code |
| n_subtaxa_1.Taxonomy | Source code |
| n_subtaxa_1.default | Source code |
| n_supertaxa | Man page Source code |
| n_supertaxa.Taxonomy | Source code |
| n_supertaxa.default | Source code |
| n_supertaxa_1 | Man page Source code |
| n_supertaxa_1.Taxonomy | Source code |
| n_supertaxa_1.default | Source code |
| name_font | Man page Source code |
| names_used | Man page |
| ncbi_sequence | Man page |
| ncbi_taxon_sample | Man page Source code |
| nms | Man page Source code |
| num_range | Man page |
| obs | Man page Source code |
| obs.Taxmap | Source code |
| obs.default | Source code |
| obs_apply | Man page Source code |
| obs_apply.Taxmap | Source code |
| obs_apply.default | Source code |
| one_of | Man page |
| parse_dada2 | Man page Source code |
| parse_dataset | Man page Source code |
| parse_edge_list | Man page Source code Source code |
| parse_greengenes | Man page Source code |
| parse_heirarchies_to_taxonomy | Man page Source code |
| parse_mothur_tax_summary | Man page Source code |
| parse_mothur_taxonomy | Man page Source code |
| parse_newick | Man page Source code |
| parse_phylo | Man page Source code |
| parse_phyloseq | Man page Source code |
| parse_possibly_named_logical | Man page Source code |
| parse_primersearch | Man page Source code |
| parse_qiime_biom | Man page Source code |
| parse_raw_heirarchies_to_taxonomy | Man page Source code |
| parse_rdp | Man page Source code |
| parse_seq_input | Man page Source code |
| parse_silva_fasta | Man page Source code |
| parse_summary_seqs | Man page Source code |
| parse_tax_data | Man page Source code |
| parse_ubiome | Man page Source code |
| parse_unite_general | Man page Source code |
| polygon_coords | Man page Source code |
| prefixed_print | Man page Source code |
| primersearch | Man page Source code |
| primersearch_is_installed | Man page Source code |
| primersearch_raw | Man page Source code |
| print.hierarchies | Source code |
| print.taxa | Source code |
| print.taxapicker | Source code |
| print__character | Man page Source code |
| print__data.frame | Man page Source code |
| print__default_ | Man page Source code |
| print__factor | Man page Source code |
| print__integer | Man page Source code |
| print__list | Man page Source code |
| print__logical | Man page Source code |
| print__matrix | Man page Source code |
| print__numeric | Man page Source code |
| print__ordered | Man page Source code |
| print__tbl_df | Man page Source code |
| print__vector | Man page Source code |
| print_item | Man page Source code |
| print_tree | Man page Source code |
| print_tree.Taxonomy | Source code |
| print_tree.default | Source code |
| progress_lapply | Man page Source code |
| punc_font | Man page Source code |
| qualitative_palette | Man page Source code |
| quantative_palette | Man page Source code |
| rad_to_deg | Source code |
| ranks | Man page Source code |
| ranks_ref | Man page |
| rarefy_obs | Man page Source code |
| read_fasta | Man page Source code |
| read_lines_apply | Man page Source code |
| remove_redundant_names | Man page Source code |
| remove_redundant_names.Taxonomy | Source code |
| remove_redundant_names.default | Source code |
| repel_boxes | Source code |
| replace_taxon_ids | Man page Source code |
| replace_taxon_ids.Taxonomy | Source code |
| replace_taxon_ids.default | Source code |
| repo_url | Man page Source code |
| rescale | Man page |
| rev_comp | Man page Source code |
| reverse | Man page Source code |
| roots | Man page Source code |
| roots.Taxonomy | Source code |
| roots.default | Source code |
| run_primersearch | Man page Source code |
| sample_frac_obs | Man page Source code |
| sample_frac_obs.Taxmap | Source code |
| sample_frac_obs.default | Source code |
| sample_frac_taxa | Man page Source code |
| sample_frac_taxa.Taxmap | Source code |
| sample_frac_taxa.Taxonomy | Source code |
| sample_frac_taxa.default | Source code |
| sample_n_obs | Man page Source code |
| sample_n_obs.Taxmap | Source code |
| sample_n_obs.default | Source code |
| sample_n_taxa | Man page Source code |
| sample_n_taxa.Taxmap | Source code |
| sample_n_taxa.Taxonomy | Source code |
| sample_n_taxa.default | Source code |
| scale_bar_coords | Man page Source code |
| select_labels | Man page Source code |
| select_obs | Man page Source code |
| select_obs.Taxmap | Source code |
| select_obs.default | Source code |
| simplify | Man page Source code |
| split_by_level | Man page Source code |
| starts_with | Man page |
| startup_msg | Man page Source code |
| stems | Man page Source code |
| stems.Taxonomy | Source code |
| stems.default | Source code |
| strex | Source code |
| subtaxa | Man page Source code |
| subtaxa.Taxonomy | Source code |
| subtaxa.default | Source code |
| subtaxa_apply | Man page Source code |
| subtaxa_apply.Taxonomy | Source code |
| subtaxa_apply.default | Source code |
| supertaxa | Man page Source code |
| supertaxa.Taxonomy | Source code |
| supertaxa.default | Source code |
| supertaxa_apply | Man page Source code |
| supertaxa_apply.Taxonomy | Source code |
| supertaxa_apply.default | Source code |
| taxa | Man page Source code |
| taxa-package | Man page |
| taxmap | Man page Source code |
| taxon | Man page Source code |
| taxon_database | Man page Source code |
| taxon_id | Man page Source code |
| taxon_ids | Man page Source code |
| taxon_ids.Taxonomy | Source code |
| taxon_ids.default | Source code |
| taxon_indexes | Man page Source code |
| taxon_indexes.Taxonomy | Source code |
| taxon_indexes.default | Source code |
| taxon_name | Man page Source code |
| taxon_names | Man page Source code |
| taxon_names.Taxonomy | Source code |
| taxon_names.default | Source code |
| taxon_rank | Man page Source code |
| taxon_ranks | Man page Source code |
| taxon_ranks.Taxonomy | Source code |
| taxon_ranks.default | Source code |
| taxonomy | Man page Source code |
| taxonomy_table | Man page Source code |
| taxonomy_table.Taxonomy | Source code |
| taxonomy_table.default | Source code |
| text_grob_length | Man page Source code |
| tid_font | Man page Source code |
| to_percent | Man page Source code |
| transform_data | Man page Source code |
| transmute_obs | Man page Source code |
| transmute_obs.Taxmap | Source code |
| transmute_obs.default | Source code |
| unique_mapping | Man page Source code Source code |
| validate_regex_key_pair | Man page Source code |
| validate_regex_match | Man page Source code |
| validate_taxmap_funcs | Man page Source code |
| verify_color_range | Man page Source code |
| verify_label_count | Man page Source code |
| verify_size | Man page Source code |
| verify_size_range | Man page Source code |
| verify_taxmap | Man page Source code |
| verify_trans | Man page Source code |
| which_ranks | Source code |
| write_greengenes | Man page Source code |
| write_mothur_taxonomy | Man page Source code |
| write_rdp | Man page Source code |
| write_silva_fasta | Man page Source code |
| write_unite_general | Man page Source code |
| zero_low_counts | Man page Source code |
