Files in metacoder

Tools for Parsing, Manipulating, and Graphing Taxonomic Abundance Data

NEWS.md README.md R/RcppExports.R R/old_taxa--dataset_documentation.R R/old_taxa--taxmap--option_parsers.R R/heat_tree--legend.R R/old_taxa--globals.R R/old_taxa--taxon_id.R R/old_taxa--taxmap--internal.R R/mothur.R R/internal.R R/old_taxa--hierarchies.R R/heat_tree--resizing_text.R R/metacoder-package.R R/old_taxa--taxonomy--internal.R R/old_taxa--package.R R/heat_tree--internal.R R/heat_tree_matrix.R R/old_taxa--temp.R R/old_taxa--lazyhelpers.R R/heat_tree--mapping.R R/option_parsers.R R/old_taxa--taxmap--parsers.R R/old_taxa--taxmap--class.R R/old_taxa--taxonomy--class.R R/heat_tree.R R/parsers.R R/dataset_documentation.R R/old_taxa--taxon.R R/old_taxa--taxmap--s3.R R/old_taxa--imports.R R/remove_ambiguous.R R/read_fasta.R R/old_taxa--zzz.R R/old_taxa--taxonomy--docs.R R/tools.R R/old_taxa--internal.R R/heat_tree--vertex_size.R R/old_taxa--taxon_database.R R/old_taxa--taxon_name.R R/calculations--internal.R R/old_taxa--taxa.R R/old_taxa--taxmap--docs.R R/primersearch.R R/calculations.R R/old_taxa--taxonomy--s3.R R/old_taxa--taxmap--printers.R R/calculations--differential_abundance.R R/as_phyloseq.R R/old_taxa--taxon_rank.R R/old_taxa--hierarchy.R R/imports.R R/heat_tree--shape_generators.R R/startup.R R/sequence_download.R R/heat_tree--layouts.R R/writers.R inst/doc/introduction.Rmd tests/testthat.R tests/testthat/test--calculations.R tests/testthat/test-taxon_id.R tests/testthat/test--taxmap_parsers.R tests/testthat/test--taxonomy.R tests/testthat/test--taxa.R tests/testthat/test--heat_tree.R tests/testthat/test--parsers_and_writers.R tests/testthat/test-taxon.R tests/testthat/test--simulated_pcr.R tests/testthat/test-taxon_rank.R tests/testthat/test--taxmap.R tests/testthat/test-taxon_name.R vignettes/introduction.Rmd man/leaves.Rd man/my_print.Rd man/DNAbin_to_char.Rd man/n_leaves_1.Rd man/add_alpha.Rd man/taxa-package.Rd man/read_fasta.Rd man/can_be_used_in_taxmap.Rd man/get_database_name.Rd man/read_lines_apply.Rd man/check_taxmap_data.Rd man/transmute_obs.Rd man/get_expected_data.Rd man/parse_raw_heirarchies_to_taxonomy.Rd man/sample_frac_taxa.Rd man/quantative_palette.Rd man/validate_taxmap_funcs.Rd man/calc_n_samples.Rd man/validate_regex_match.Rd man/make_fasta_with_u_replaced.Rd man/desc_font.Rd man/ex_taxmap.Rd man/n_supertaxa_1.Rd man/scale_bar_coords.Rd man/starts_with.Rd man/write_rdp.Rd man/do_calc_on_num_cols.Rd man/parse_silva_fasta.Rd man/ranks_ref.Rd man/get_taxmap_cols.Rd man/to_percent.Rd man/parse_greengenes.Rd man/count_capture_groups.Rd man/print__matrix.Rd man/parse_phyloseq.Rd man/taxon.Rd man/sample_frac_obs.Rd man/rarefy_obs.Rd man/get_class_from_el.Rd man/print__logical.Rd man/primersearch_raw.Rd man/select_obs.Rd man/make_dada2_tax_table.Rd man/ambiguous_patterns.Rd man/counts_to_presence.Rd man/calc_obs_props.Rd man/classifications.Rd man/print__default_.Rd man/parse_possibly_named_logical.Rd man/parse_ubiome.Rd man/reverse.Rd man/print_item.Rd man/init_taxmap_data.Rd man/edge_list_depth.Rd man/sample_n_obs.Rd man/line_coords.Rd man/is_ambiguous.Rd man/make_plot_legend.Rd man/calc_prop_samples.Rd man/convert_base.Rd man/is_branch.Rd man/taxonomy_table.Rd man/hmp_otus.Rd man/extract_tax_data.Rd man/hierarchy.Rd man/contains.Rd man/taxon_id.Rd man/all_functions.Rd man/write_greengenes.Rd man/taxon_ranks.Rd man/verify_label_count.Rd man/replace_taxon_ids.Rd man/polygon_coords.Rd man/supertaxa.Rd man/parse_unite_general.Rd man/taxonomy.Rd man/verify_size_range.Rd man/progress_lapply.Rd man/taxon_rank.Rd man/id_classifications.Rd man/parse_primersearch.Rd man/obs.Rd man/inverse.Rd man/print__numeric.Rd man/length_of_thing.Rd man/make_dada2_asv_table.Rd man/taxon_names.Rd man/highlight_taxon_ids.Rd man/get_data.Rd man/fasta_headers.Rd man/get_sort_var.Rd man/n_supertaxa.Rd man/validate_regex_key_pair.Rd man/parse_seq_input.Rd man/text_grob_length.Rd man/error_font.Rd man/rescale.Rd man/name_font.Rd man/verify_size.Rd man/ex_hierarchy2.Rd man/get_taxmap_other_cols.Rd man/print_tree.Rd man/primersearch_is_installed.Rd man/dot-onAttach.Rd man/matches.Rd man/get_node_children.Rd man/taxa.Rd man/ex_hierarchies.Rd man/map_unique.Rd man/multi_sep_split.Rd man/capitalize.Rd man/print__character.Rd man/split_by_level.Rd man/taxon_indexes.Rd man/molten_dist.Rd man/parse_tax_data.Rd man/arrange_taxa.Rd man/calc_taxon_abund.Rd man/database_list.Rd man/map_data.Rd man/subtaxa.Rd man/print__integer.Rd man/check_option_groups.Rd man/internodes.Rd man/parse_phylo.Rd man/filter_ambiguous_taxa.Rd man/select_labels.Rd man/sample_n_taxa.Rd man/print__tbl_df.Rd man/map_data_.Rd man/n_leaves.Rd man/n_subtaxa.Rd man/get_taxmap_table.Rd man/parse_newick.Rd man/simplify.Rd man/look_for_na.Rd man/label_bounds.Rd man/rev_comp.Rd man/get_taxmap_data.Rd man/layout_functions.Rd man/apply_color_scale.Rd man/unique_mapping.Rd man/limited_print.Rd man/calc_group_median.Rd man/parse_heirarchies_to_taxonomy.Rd man/calc_group_stat.Rd man/grapes-greater-than-grapes.Rd man/parse_dataset.Rd man/as_id.Rd man/mutate_obs.Rd man/write_unite_general.Rd man/n_obs_1.Rd man/tid_font.Rd man/taxmap.Rd man/is_internode.Rd man/parse_qiime_biom.Rd man/parse_dada2.Rd man/parse_edge_list.Rd man/get_data_frame.Rd man/obs_apply.Rd man/stems.Rd man/verify_taxmap.Rd man/get_numerics.Rd man/check_for_pkg.Rd man/one_of.Rd man/get_numeric_cols.Rd man/remove_redundant_names.Rd man/print__vector.Rd man/is_root.Rd man/taxon_name.Rd man/startup_msg.Rd man/hmp_samples.Rd man/parse_summary_seqs.Rd man/qualitative_palette.Rd man/data_used.Rd man/run_primersearch.Rd man/ex_hierarchy3.Rd man/print__factor.Rd man/roots.Rd man/zero_low_counts.Rd man/filter_obs.Rd man/is_stem.Rd man/lookup_tax_data.Rd man/hierarchies.Rd man/n_obs.Rd man/compare_groups.Rd man/taxon_database.Rd man/names_used.Rd man/verify_trans.Rd man/ambiguous_synonyms.Rd man/get_optimal_range.Rd man/parse_rdp.Rd man/prefixed_print.Rd man/num_range.Rd man/write_silva_fasta.Rd man/subtaxa_apply.Rd man/all_names.Rd man/primersearch.Rd man/calc_group_mean.Rd man/supertaxa_apply.Rd man/ends_with.Rd man/ncbi_sequence.Rd man/leaves_apply.Rd man/diverging_palette.Rd man/ex_hierarchy1.Rd man/get_taxonomy_levels.Rd man/heat_tree_matrix.Rd man/complement.Rd man/ncbi_taxon_sample.Rd man/can_be_num.Rd man/punc_font.Rd man/transform_data.Rd man/taxon_ids.Rd man/n_subtaxa_1.Rd man/check_element_length.Rd man/verify_color_range.Rd man/metacoder.Rd man/heat_tree.Rd man/correct_taxon_names.Rd man/calc_group_rsd.Rd man/get_dataset.Rd man/repo_url.Rd man/get_edge_children.Rd man/is_leaf.Rd man/get_edge_parents.Rd man/arrange_obs.Rd man/print__ordered.Rd man/filter_taxa.Rd man/print__list.Rd man/parse_mothur_taxonomy.Rd man/as_phyloseq.Rd man/print__data.frame.Rd man/check_class_col.Rd man/filtering-helpers.Rd man/calc_diff_abund_deseq2.Rd man/inter_circle_gap.Rd man/get_dots_or_list.Rd man/branches.Rd man/write_mothur_taxonomy.Rd man/parse_mothur_tax_summary.Rd man/everything.Rd