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).

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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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