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 | |
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Vignettes of metacoder
Name | ||
introduction.Rmd | ||
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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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