metacoder v0.1.3
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Tools for Parsing, Manipulating, and Graphing Hierarchical Data
A set of tools for parsing, manipulating, and graphing data classified by a hierarchy (e.g. a taxonomy).
Readme
An R package for metabarcoding research planning and analysis
Metabarcoding is revolutionizing microbial ecology and presenting new challenges:
- Numerous database formats make taxonomic data difficult to parse, combine, and subset.
- Stacked bar charts, commonly used to depict community diversity, lack taxonomic context.
- Barcode loci and primers are a source of under-explored bias.
Metacoder is an R package that attempts to addresses these issues:
- Sources of taxonomic data can be extracted from most file formats and manipulated.
- Community diversity can be visualized by color and size in a tree plot.
- Primer specificity can be estimated with in silico PCR.
Documentation
Documentation is available at http://grunwaldlab.github.io/metacoder_documentation.
Download the current version
Stable releases are available on CRAN and can be installed in the standard way:
install.packages("metacoder")
The most recent version can be installed from Github:
devtools::install_github("grunwaldlab/metacoder@dev")
library(metacoder)
Dependencies
The function that runs in silico PCR requires primersearch from the EMBOSS tool kit to be installed. This is not an R package, so it is not automatically installed. Type ?primersearch after installing and loading MetcodeR for installation instructions.
Citation
If you use metcoder in a publication, please cite our article in PLOS Computational Biology:
Foster ZSL, Sharpton TJ, Grünwald NJ (2017) Metacoder: An R package for visualization and manipulation of community taxonomic diversity data. PLOS Computational Biology 13(2): e1005404. https://doi.org/10.1371/journal.pcbi.1005404
License
This work is subject to the MIT License.
Functions in metacoder
| Name | Description | |
| arrange_taxa | Sort columns of taxmap objects | |
| class_from_class | Parse embedded classifications | |
| class_from_name | Retrieve classifications from taxon names | |
| bryophytes_ex_data | Example dataset of bryophytes | |
| class_to_taxonomy | List of classifications to taxonomy tree | |
| contains | dplyr select_helpers | |
| genbank_ex_data | Fungal ITS Genbank refseq | |
| count_capture_groups | Count capture groups | |
| delete_vetices_and_children | delete_vetices_and_children | |
| %>% | magrittr forward-pipe operator | |
| heat_tree | Plot a taxonomic tree | |
| line_coords | Makes coordinates for a line | |
| make_new_ids | Generate new unique IDs | |
| n_obs | Count observations in taxmap | |
| n_obs_1 | Count observation assigned in taxmap | |
| postDrawDetails.resizingTextGrob | Clean up after the drawing. | |
| pr2_ex_data | Example of PR2 SSU data | |
| get_class_from_el | Get classification for taxa in edge list | |
| get_node_children | get_node_children | |
| get_numerics | Return numeric values in a character | |
| split_by_level | Splits a taxonomy at a specific level or rank | |
| text_grob_length | Estimate text grob length | |
| transform_data | Transformation functions | |
| verify_color_range | Verify color range parameters | |
| verify_label_count | Verify label count | |
| rdp_ex_data | Example of RDP Archea data | |
| read_fasta | Read a FASTA file | |
| roots | Get root taxa | |
| run_primersearch | Execute EMBOSS Primerseach | |
| silva_ex_data | Example dataset from SILVA | |
| label_bounds | Bounding box coords for labels | |
| layout_functions | Layout functions | |
| map_unique | Run a function on unique values of a iterable | |
| matches | dplyr select_helpers | |
| n_supertaxa | Get number of supertaxa | |
| ncbi_sequence | Downloads sequences from ids | |
| taxmap | Create an instance of taxmap | |
| taxon_data | Return taxon data from taxmap | |
| transmute_obs | Replace columns in taxmap objects | |
| transmute_taxa | Replace columns in taxmap objects | |
| unite_ex_data_2 | Example of UNITE fungal ITS data | |
| unite_ex_data_3 | Example of UNITE fungal ITS data | |
| get_edge_children | get_edge_children | |
| get_edge_parents | get_edge_parents | |
| hierarchies | Get classification of taxa | |
| inter_circle_gap | Finds the gap/overlap of circle coordinates | |
| metacoder | Metacoder | |
| molten_dist | Get all distances between points | |
| sample_frac_obs | Sample a proportion of observations from taxmap | |
| sample_frac_taxa | Sample a proportion of taxa from taxmap | |
| select_obs | Subset columns in a taxmap object | |
| select_taxa | Subset columns in a taxmap object | |
| validate_regex_key_pair | Check a regex-key pair | |
| validate_regex_match | Check that all match input | |
| apply_color_scale | Covert numbers to colors | |
| arrange_obs | Sort columns of taxmap objects | |
| contaminants | Example dataset of contamination | |
| convert_numeric_cols | Convert columns to numeric if appropriate | |
| filter_taxa | Filter taxa with a list of conditions | |
| format_taxon_subset | Format taxon subset value | |
| make_plot_legend | Make color/size legend | |
| make_text_grobs | Create a list of text grobs | |
| one_of | dplyr select_helpers | |
| parse_hmp_qiime | Parse HMP QIIME results | |
| parse_summary_seqs | Parse summary.seqs output | |
| parse_taxonomy_table | Parse taxonomic data in a tsv/csv file | |
| primersearch_is_installed | Test if primersearch is installed | |
| print.taxmap | Print a taxmap object | |
| scale_bar_coords | Make scale bar division | |
| select_labels | Pick labels to show | |
| subtaxa | Get all subtaxa of a taxon | |
| supertaxa | Get all supertaxa of a taxon | |
| taxonomic_sample | Recursivly sample a set of taxonomic assignments | |
| taxonomy_ranks | Get ordered ranks from taxonomy | |
| diverging_palette | The default diverging color palette | |
| drawDetails.resizingTextGrob | Draws a resizingTextGrob | |
| everything | dplyr select_helpers | |
| extract_taxonomy | Extract taxonomy information from sequence headers | |
| ncbi_taxon_sample | Download representative sequences for a taxon | |
| num_range | dplyr select_helpers | |
| plot_alignment | Display sequence alignment | |
| polygon_coords | Makes coordinates for a regualr polygon | |
| qualitative_palette | The default qualitative color palette | |
| quantative_palette | The default quantative color palette | |
| can_be_num | Test if characters can be converted to numbers | |
| check_element_length | Check length of graph attributes | |
| class_from_obs_id | Retrieve classifications from observation IDs | |
| class_from_taxon_id | Retrieve classifications from taxon IDs | |
| fasta_headers | Get line numbers of FASTA headers | |
| filter_obs | Filter observations with a list of conditions | |
| get_id_from_name | Get taxon ID from name | |
| get_name_from_id | Get taxon name from ID | |
| preDrawDetails.resizingTextGrob | Adjusts text size to viewport | |
| primersearch | Use EMBOSS primersearch for in silico PCR | |
| read_lines_apply | Apply a function to chunks of a file | |
| recursive_sample | Recursivly sample observations with a heirarchical classification | |
| rescale | Rescale numeric vector to have specified minimum and maximum. | |
| resizingTextGrob | Adds text grob that scales with viewport size | |
| unique_mapping | get indexes of a unique set of the input | |
| unite_ex_data_1 | Example of UNITE fungal ITS data | |
| verify_trans | Verify transformation function parameters | |
| vigilant_report | Report a error/warning if needed | |
| n_subtaxa_1 | Get number of subtaxa | |
| obs | Get observations associated with taxa | |
| obs_data | Return observation data from taxmap | |
| remove_redundant_names | Remove the redundant taxon names | |
| inverse | Generate the inverse of a function | |
| its1_ex_data | Example of ITS1 fungal data | |
| n_subtaxa | Get number of subtaxa | |
| rename_duplicated | Number duplicated names | |
| sample_n_obs | Sample n observations from taxmap | |
| DNAbin_to_char | Converts DNAbin to a named character vector | |
| sample_n_taxa | Sample n taxa from taxmap | |
| add_alpha | add_alpha | |
| verify_size | Verify size parameters | |
| verify_size_range | Verify size range parameters | |
| edge_list_depth | Get distance from root of edgelist observations | |
| ends_with | dplyr select_helpers | |
| get_optimal_range | Find optimal range | |
| get_taxonomy_levels | Get taxonomy levels | |
| parse_mothur_summary | Parse mothur classification summary file | |
| parse_primersearch | Parse EMBOSS primersearch output | |
| mutate_obs | Add columns to taxmap objects | |
| mutate_taxa | Add columns to taxmap objects | |
| obs_data_colnames | Get column names of obs_data | |
| obs_data_cols_used | Get names of obs_data in an unevaluated expression | |
| split_class_list | Split a list of classifications by a row/column value | |
| taxon_data_colnames | Get column names of taxon_data | |
| taxon_data_cols_used | Get names of taxon_data in an unevaluated expression | |
| starts_with | dplyr select_helpers | |
| No Results! | ||
Vignettes of metacoder
| Name | ||
| introduction.Rmd | ||
| No Results! | ||
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Details
| License | GPL-2 | GPL-3 |
| LazyData | true |
| URL | https://grunwaldlab.github.io/metacoder_documentation/ |
| BugReports | https://github.com/grunwaldlab/metacoder/issues |
| VignetteBuilder | knitr |
| RoxygenNote | 6.0.1 |
| Date | 2017-05-22 |
| Encoding | UTF-8 |
| NeedsCompilation | no |
| Packaged | 2017-05-23 05:26:16 UTC; fosterz |
| Repository | CRAN |
| Date/Publication | 2017-05-23 05:36:48 UTC |
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