Man pages for grunwaldlab/metacoder
Tools for Parsing, Manipulating, and Graphing Taxonomic Abundance Data
| add_alpha | add_alpha |
| all_functions | Get list of usable functions |
| all_names | Return names of data in [taxonomy()] or [taxmap()] |
| ambiguous_patterns | Get patterns for ambiguous taxa |
| ambiguous_synonyms | Get patterns for ambiguous taxa |
| apply_color_scale | Covert numbers to colors |
| arrange_obs | Sort user data in [taxmap()] objects |
| arrange_taxa | Sort the edge list of [taxmap()] objects |
| as_id | Convert a vector to database IDs |
| as_phyloseq | Convert taxmap to phyloseq |
| branches | Get "branch" taxa |
| calc_diff_abund_deseq2 | Differential abundance with DESeq2 |
| calc_group_mean | Calculate means of groups of columns |
| calc_group_median | Calculate medians of groups of columns |
| calc_group_rsd | Relative standard deviations of groups of columns |
| calc_group_stat | Apply a function to groups of columns |
| calc_n_samples | Count the number of samples |
| calc_obs_props | Calculate proportions from observation counts |
| calc_prop_samples | Calculate the proportion of samples |
| calc_taxon_abund | Sum observation values for each taxon |
| can_be_num | Test if characters can be converted to numbers |
| can_be_used_in_taxmap | Check that a unknown object can be used with taxmap |
| capitalize | Capitalize |
| check_class_col | Check for name/index in input data |
| check_element_length | Check length of graph attributes |
| check_for_pkg | check for packages |
| check_option_groups | Check option: groups |
| check_taxmap_data | Check dataset format |
| classifications | Get classifications of taxa |
| compare_groups | Compare groups of samples |
| complement | Find complement of sequences |
| contains | dplyr select_helpers |
| convert_base | Converts decimal numbers to other bases |
| correct_taxon_names | Look up official names from potentially misspelled names |
| count_capture_groups | Count capture groups |
| counts_to_presence | Apply a function to groups of columns |
| database_list | Database list |
| data_used | Get values of data used in expressions |
| desc_font | Description formatting in print methods |
| diverging_palette | The default diverging color palette |
| DNAbin_to_char | Converts DNAbin to a named character vector |
| do_calc_on_num_cols | Run some function to produce new columns. |
| dot-onAttach | Run when package loads |
| edge_list_depth | Get distance from root of edgelist observations |
| ends_with | dplyr select_helpers |
| error_font | Font to indicate an error |
| everything | dplyr select_helpers |
| ex_hierarchies | An example hierarchies object |
| ex_hierarchy1 | An example Hierarchy object |
| ex_hierarchy2 | An example Hierarchy object |
| ex_hierarchy3 | An example Hierarchy object |
| ex_taxmap | An example taxmap object |
| extract_tax_data | Extracts taxonomy info from vectors with regex |
| fasta_headers | Get line numbers of FASTA headers |
| filter_ambiguous_taxa | Filter ambiguous taxon names |
| filtering-helpers | Taxonomic filtering helpers |
| filter_obs | Filter observations with a list of conditions |
| filter_taxa | Filter taxa with a list of conditions |
| get_class_from_el | Get classification for taxa in edge list |
| get_data | Get data in a taxmap object by name |
| get_database_name | Return name of database |
| get_data_frame | Get data in a taxonomy or taxmap object by name |
| get_dataset | Get a data set from a taxmap object |
| get_dots_or_list | Get input from dots or list |
| get_edge_children | get_edge_children |
| get_edge_parents | get_edge_parents |
| get_expected_data | Get a data set in as_phyloseq |
| get_node_children | get_node_children |
| get_numeric_cols | Get numeric columns from taxmap table |
| get_numerics | Return numeric values in a character |
| get_optimal_range | Find optimal range |
| get_sort_var | Get a vector from a vector/list/table to be used in mapping |
| get_taxmap_cols | Get a column subset |
| get_taxmap_data | Get a data set from a taxmap object |
| get_taxmap_other_cols | Parse the other_cols option |
| get_taxmap_table | Get a table from a taxmap object |
| get_taxonomy_levels | Get taxonomy levels |
| grapes-greater-than-grapes | magrittr forward-pipe operator |
| heat_tree | Plot a taxonomic tree |
| heat_tree_matrix | Plot a matrix of heat trees |
| hierarchies | Make a set of many [hierarchy()] class objects |
| hierarchy | The Hierarchy class |
| highlight_taxon_ids | Highlight taxon ID column |
| hmp_otus | A HMP subset |
| hmp_samples | Sample information for HMP subset |
| id_classifications | Get ID classifications of taxa |
| init_taxmap_data | Convert 'data' input for Taxamp |
| inter_circle_gap | Finds the gap/overlap of circle coordinates |
| internodes | Get "internode" taxa |
| inverse | Generate the inverse of a function |
| is_ambiguous | Find ambiguous taxon names |
| is_branch | Test if taxa are branches |
| is_internode | Test if taxa are "internodes" |
| is_leaf | Test if taxa are leaves |
| is_root | Test if taxa are roots |
| is_stem | Test if taxa are stems |
| label_bounds | Bounding box coords for labels |
| layout_functions | Layout functions |
| leaves | Get leaf taxa |
| leaves_apply | Apply function to leaves of each taxon |
| length_of_thing | Check length of thing |
| limited_print | Print a subset of a character vector |
| line_coords | Makes coordinates for a line |
| look_for_na | Look for NAs in parameters |
| lookup_tax_data | Convert one or more data sets to taxmap |
| make_dada2_asv_table | Make a imitation of the dada2 ASV abundance matrix |
| make_dada2_tax_table | Make a imitation of the dada2 taxonomy matrix |
| make_fasta_with_u_replaced | Make a temporary file U's replaced with T |
| make_plot_legend | Make color/size legend |
| map_data | Create a mapping between two variables |
| map_data_ | Create a mapping without NSE |
| map_unique | Run a function on unique values of a iterable |
| matches | dplyr select_helpers |
| metacoder | Metacoder |
| molten_dist | Get all distances between points |
| multi_sep_split | Like 'strsplit', but with multiple separators |
| mutate_obs | Add columns to [taxmap()] objects |
| my_print | Print something |
| name_font | Variable name formatting in print methods |
| names_used | Get names of data used in expressions |
| ncbi_sequence | Downloads sequences from ids |
| ncbi_taxon_sample | Download representative sequences for a taxon |
| n_leaves | Get number of leaves |
| n_leaves_1 | Get number of leaves |
| n_obs | Count observations in [taxmap()] |
| n_obs_1 | Count observation assigned in [taxmap()] |
| n_subtaxa | Get number of subtaxa |
| n_subtaxa_1 | Get number of subtaxa |
| n_supertaxa | Get number of supertaxa |
| n_supertaxa_1 | Get number of supertaxa |
| num_range | dplyr select_helpers |
| obs | Get data indexes associated with taxa |
| obs_apply | Apply function to observations per taxon |
| one_of | dplyr select_helpers |
| parse_dada2 | Convert the output of dada2 to a taxmap object |
| parse_dataset | Parse options specifying datasets |
| parse_edge_list | Convert a table with an edge list to taxmap |
| parse_greengenes | Parse Greengenes release |
| parse_heirarchies_to_taxonomy | Infer edge list from hierarchies |
| parse_mothur_taxonomy | Parse mothur Classify.seqs *.taxonomy output |
| parse_mothur_tax_summary | Parse mothur *.tax.summary Classify.seqs output |
| parse_newick | Parse a Newick file |
| parse_phylo | Parse a phylo object |
| parse_phyloseq | Convert a phyloseq to taxmap |
| parse_possibly_named_logical | used to parse inputs to 'drop_obs' and 'reassign_obs' |
| parse_primersearch | Parse EMBOSS primersearch output |
| parse_qiime_biom | Parse a BIOM output from QIIME |
| parse_raw_heirarchies_to_taxonomy | Infer edge list from hierarchies composed of character... |
| parse_rdp | Parse RDP FASTA release |
| parse_seq_input | Read sequences in an unknown format |
| parse_silva_fasta | Parse SILVA FASTA release |
| parse_summary_seqs | Parse summary.seqs output |
| parse_tax_data | Convert one or more data sets to taxmap |
| parse_ubiome | Converts the uBiome file format to taxmap |
| parse_unite_general | Parse UNITE general release FASTA |
| polygon_coords | Makes coordinates for a regular polygon |
| prefixed_print | Print a object with a prefix |
| primersearch | Use EMBOSS primersearch for in silico PCR |
| primersearch_is_installed | Test if primersearch is installed |
| primersearch_raw | Use EMBOSS primersearch for in silico PCR |
| print__character | Print a character |
| print__data.frame | Print a data.frame |
| print__default_ | Print method for unsupported |
| print__factor | Print a factor |
| print__integer | Print an integer |
| print_item | Print a item |
| print__list | Print a list |
| print__logical | Print a logical |
| print__matrix | Print a matrix |
| print__numeric | Print a numeric |
| print__ordered | Print a ordered factor |
| print__tbl_df | Print a tibble |
| print_tree | Print a text tree |
| print__vector | Generic vector printer |
| progress_lapply | lappy with progress bars |
| punc_font | Punctuation formatting in print methods |
| qualitative_palette | The default qualitative color palette |
| quantative_palette | The default quantative color palette |
| ranks_ref | Lookup-table for IDs of taxonomic ranks |
| rarefy_obs | Calculate rarefied observation counts |
| read_fasta | Read a FASTA file |
| read_lines_apply | Apply a function to chunks of a file |
| remove_redundant_names | Remove redundant parts of taxon names |
| replace_taxon_ids | Replace taxon ids |
| repo_url | Return github url |
| rescale | Rescale numeric vector to have specified minimum and maximum. |
| rev_comp | Revere complement sequences |
| reverse | Reverse sequences |
| roots | Get root taxa |
| run_primersearch | Execute EMBOSS Primersearch |
| sample_frac_obs | Sample a proportion of observations from [taxmap()] |
| sample_frac_taxa | Sample a proportion of taxa from [taxonomy()] or [taxmap()] |
| sample_n_obs | Sample n observations from [taxmap()] |
| sample_n_taxa | Sample n taxa from [taxonomy()] or [taxmap()] |
| scale_bar_coords | Make scale bar division |
| select_labels | Pick labels to show |
| select_obs | Subset columns in a [taxmap()] object |
| simplify | List to vector of unique elements |
| split_by_level | Splits a taxonomy at a specific level or rank |
| starts_with | dplyr select_helpers |
| startup_msg | Return startup message |
| stems | Get stem taxa |
| subtaxa | Get subtaxa |
| subtaxa_apply | Apply function to subtaxa of each taxon |
| supertaxa | Get all supertaxa of a taxon |
| supertaxa_apply | Apply function to supertaxa of each taxon |
| taxa | A class for multiple taxon objects |
| taxmap | Taxmap class |
| taxon | Taxon class |
| taxon_database | Taxonomy database class |
| taxon_id | Taxon ID class |
| taxon_ids | Get taxon IDs |
| taxon_indexes | Get taxon indexes |
| taxon_name | Taxon name class |
| taxon_names | Get taxon names |
| taxonomy | Taxonomy class |
| taxonomy_table | Convert taxonomy info to a table |
| taxon_rank | Taxon rank class |
| taxon_ranks | Get taxon ranks |
| text_grob_length | Estimate text grob length |
| tid_font | Taxon id formatting in print methods |
| to_percent | Format a proportion as a printed percent |
| transform_data | Transformation functions |
| transmute_obs | Replace columns in [taxmap()] objects |
| unique_mapping | get indexes of a unique set of the input |
| validate_regex_key_pair | Check a regex-key pair |
| validate_regex_match | Check that all match input |
| validate_taxmap_funcs | Validate 'funcs' input for Taxamp |
| verify_color_range | Verify color range parameters |
| verify_label_count | Verify label count |
| verify_size | Verify size parameters |
| verify_size_range | Verify size range parameters |
| verify_taxmap | Check that an object is a taxmap |
| verify_trans | Verify transformation function parameters |
| write_greengenes | Write an imitation of the Greengenes database |
| write_mothur_taxonomy | Write an imitation of the Mothur taxonomy file |
| write_rdp | Write an imitation of the RDP FASTA database |
| write_silva_fasta | Write an imitation of the SILVA FASTA database |
| write_unite_general | Write an imitation of the UNITE general FASTA database |
| zero_low_counts | Replace low counts with zero |
