Package: metacoder 0.3.7

Zachary Foster

metacoder: Tools for Parsing, Manipulating, and Graphing Taxonomic Abundance Data

A set of tools for parsing, manipulating, and graphing data classified by a hierarchy (e.g. a taxonomy).

Authors:Zachary Foster [aut, cre], Niklaus Grunwald [ths], Rob Gilmore [ctb]

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metacoder/json (API)
NEWS

# Install 'metacoder' in R:

install.packages('metacoder', repos = c('https://grunwaldlab.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/grunwaldlab/metacoder/issues

Uses libs:

c++– GNU Standard C++ Library v3

Datasets:

ex_taxmap - An example taxmap object
hmp_otus - A HMP subset
hmp_samples - Sample information for HMP subset
ranks_ref - Lookup-table for IDs of taxonomic ranks

On CRAN:

community-diversity hierarchical metabarcoding pcr taxonomy trees

9.17 score 136 stars 314 scripts 204 downloads 32 mentions 128 exports 141 dependencies

Last updated 9 months agofrom:54ef8eabc5. Checks:OK: 1 NOTE: 8. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 16 2024
R-4.5-win-x86_64	NOTE	Sep 17 2024
R-4.5-linux-x86_64	NOTE	Nov 16 2024
R-4.4-win-x86_64	NOTE	Sep 17 2024
R-4.4-mac-x86_64	NOTE	Sep 17 2024
R-4.4-mac-aarch64	NOTE	Sep 17 2024
R-4.3-win-x86_64	NOTE	Sep 17 2024
R-4.3-mac-x86_64	NOTE	Sep 17 2024
R-4.3-mac-aarch64	NOTE	Sep 17 2024

Exports:%>%all_names ambiguous_synonyms arrange_obs arrange_taxa as_phyloseq branches calc_diff_abund_deseq2 calc_group_mean calc_group_median calc_group_rsd calc_group_stat calc_n_samples calc_obs_props calc_prop_samples calc_taxon_abund classifications compare_groups complement contains counts_to_presence database_list diverging_palette ends_with everything extract_tax_data filter_ambiguous_taxa filter_obs filter_taxa get_data get_data_frame get_dataset heat_tree heat_tree_matrix hierarchies hierarchy id_classifications ids internodes is_ambiguous is_branch is_internode is_leaf is_root is_stem layout_functions leaves leaves_apply lookup_tax_data make_dada2_asv_table make_dada2_tax_table map_data map_data_matches mutate_obs n_leaves n_leaves_1 n_obs n_obs_1 n_subtaxa n_subtaxa_1 n_supertaxa n_supertaxa_1 ncbi_taxon_sample nms num_range obs obs_apply one_of parse_dada2 parse_edge_list parse_greengenes parse_mothur_tax_summary parse_mothur_taxonomy parse_newick parse_phylo parse_phyloseq parse_primersearch parse_qiime_biom parse_rdp parse_silva_fasta parse_tax_data parse_ubiome parse_unite_general primersearch primersearch_raw print_tree qualitative_palette quantative_palette ranks rarefy_obs read_fasta remove_redundant_names replace_taxon_ids rev_comp reverse roots sample_frac_obs sample_frac_taxa sample_n_obs sample_n_taxa select_obs starts_with stems subtaxa subtaxa_apply supertaxa supertaxa_apply taxa taxmap taxon taxon_database taxon_id taxon_ids taxon_indexes taxon_name taxon_names taxon_rank taxon_ranks taxonomy taxonomy_table transmute_obs write_greengenes write_mothur_taxonomy write_rdp write_silva_fasta write_unite_general zero_low_counts

Dependencies:ade4 ape askpass assertthat backports base64enc bit bit64 bitops bslib cachem checkmate cli clipr cluster codetools colorspace commonmark conditionz cowplot cpp11 crayon crul curl data.table digest dplyr evaluate fansi farver fastmap fastmatch fontawesome foreach foreign Formula fs GA generics ggfittext ggplot2 glue gridExtra gridtext gtable highr Hmisc hms htmlTable htmltools htmlwidgets httpcode httr igraph isoband iterators jpeg jquerylib jsonlite knitr labeling lattice lazyeval lifecycle magrittr markdown MASS Matrix memoise mgcv mime munsell natserv nlme nnet openssl pbapply permute phangorn pillar pixmap pkgconfig plyr png prettyunits progress purrr quadprog R6 rappdirs ratelimitr RColorBrewer Rcpp RcppArmadillo RCurl readr rentrez rex ritis rlang rmarkdown rncl rotl rpart rredlist rstudioapi sass scales segmented seqinr shades solrium sp stringi stringr sys taxize tibble tidyselect tinytex triebeard tzdb urltools utf8 uuid vctrs vegan viridis viridisLite vroom WikidataQueryServiceR WikidataR WikipediR wikitaxa withr worrms xfun XML xml2 yaml zoo

Documentation for metacoder

Rendered fromintroduction.Rmdusingknitr::rmarkdownon Nov 16 2024.

Last update: 2021-06-23
Started: 2016-04-11

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Return names of data in [taxonomy()] or [taxmap()]	all_names
Get patterns for ambiguous taxa	ambiguous_synonyms
Sort user data in [taxmap()] objects	arrange_obs
Sort the edge list of [taxmap()] objects	arrange_taxa
Convert taxmap to phyloseq	as_phyloseq
Get "branch" taxa	branches
Differential abundance with DESeq2	calc_diff_abund_deseq2
Calculate means of groups of columns	calc_group_mean
Calculate medians of groups of columns	calc_group_median
Relative standard deviations of groups of columns	calc_group_rsd
Apply a function to groups of columns	calc_group_stat
Count the number of samples	calc_n_samples
Calculate proportions from observation counts	calc_obs_props
Calculate the proportion of samples	calc_prop_samples
Get classifications of taxa	classifications
Compare groups of samples	compare_groups
Find complement of sequences	complement
Apply a function to groups of columns	counts_to_presence
Database list	database_list
The default diverging color palette	diverging_palette
An example hierarchies object	ex_hierarchies
An example Hierarchy object	ex_hierarchy1
An example Hierarchy object	ex_hierarchy2
An example Hierarchy object	ex_hierarchy3
An example taxmap object	ex_taxmap
Extracts taxonomy info from vectors with regex	extract_tax_data
Filter ambiguous taxon names	filter_ambiguous_taxa
Filter observations with a list of conditions	filter_obs
Filter taxa with a list of conditions	filter_taxa
Taxonomic filtering helpers	filtering-helpers ids nms ranks
Get data in a taxmap object by name	get_data
Get data in a taxonomy or taxmap object by name	get_data_frame
Get a data set from a taxmap object	get_dataset
Plot a taxonomic tree	heat_tree heat_tree.default heat_tree.Taxmap
Plot a matrix of heat trees	heat_tree_matrix
Make a set of many [hierarchy()] class objects	hierarchies
The Hierarchy class	hierarchy
Highlight taxon ID column	highlight_taxon_ids
A HMP subset	hmp_otus
Sample information for HMP subset	hmp_samples
Get ID classifications of taxa	id_classifications
Get "internode" taxa	internodes
Find ambiguous taxon names	is_ambiguous
Test if taxa are branches	is_branch
Test if taxa are "internodes"	is_internode
Test if taxa are leaves	is_leaf
Test if taxa are roots	is_root
Test if taxa are stems	is_stem
Layout functions	layout_functions
Get leaf taxa	leaves
Apply function to leaves of each taxon	leaves_apply
Convert one or more data sets to taxmap	lookup_tax_data
Make a imitation of the dada2 ASV abundance matrix	make_dada2_asv_table
Make a imitation of the dada2 taxonomy matrix	make_dada2_tax_table
Create a mapping between two variables	map_data
Create a mapping without NSE	map_data_
Metacoder	metacoder
Add columns to [taxmap()] objects	mutate_obs
Get number of leaves	n_leaves
Get number of leaves	n_leaves_1
Count observations in [taxmap()]	n_obs
Count observation assigned in [taxmap()]	n_obs_1
Get number of subtaxa	n_subtaxa
Get number of subtaxa	n_subtaxa_1
Get number of supertaxa	n_supertaxa
Get number of supertaxa	n_supertaxa_1
Download representative sequences for a taxon	ncbi_taxon_sample
Get data indexes associated with taxa	obs
Apply function to observations per taxon	obs_apply
Convert the output of dada2 to a taxmap object	parse_dada2
Parse Greengenes release	parse_greengenes
Parse mothur *.tax.summary Classify.seqs output	parse_mothur_tax_summary
Parse mothur Classify.seqs *.taxonomy output	parse_mothur_taxonomy
Parse a Newick file	parse_newick
Parse a phylo object	parse_phylo
Convert a phyloseq to taxmap	parse_phyloseq
Parse EMBOSS primersearch output	parse_primersearch
Parse a BIOM output from QIIME	parse_qiime_biom
Parse RDP FASTA release	parse_rdp
Parse SILVA FASTA release	parse_silva_fasta
Convert one or more data sets to taxmap	parse_tax_data
Converts the uBiome file format to taxmap	parse_ubiome
Parse UNITE general release FASTA	parse_unite_general
Use EMBOSS primersearch for in silico PCR	primersearch
Use EMBOSS primersearch for in silico PCR	primersearch_raw
Print a text tree	print_tree
The default qualitative color palette	qualitative_palette
The default quantative color palette	quantative_palette
Lookup-table for IDs of taxonomic ranks	ranks_ref
Calculate rarefied observation counts	rarefy_obs
Read a FASTA file	read_fasta
Remove redundant parts of taxon names	remove_redundant_names
Replace taxon ids	replace_taxon_ids
Revere complement sequences	rev_comp
Reverse sequences	reverse
Get root taxa	roots
Sample a proportion of observations from [taxmap()]	sample_frac_obs
Sample a proportion of taxa from [taxonomy()] or [taxmap()]	sample_frac_taxa
Sample n observations from [taxmap()]	sample_n_obs
Sample n taxa from [taxonomy()] or [taxmap()]	sample_n_taxa
Subset columns in a [taxmap()] object	select_obs
Get stem taxa	stems
Get subtaxa	subtaxa
Apply function to subtaxa of each taxon	subtaxa_apply
Get all supertaxa of a taxon	supertaxa
Apply function to supertaxa of each taxon	supertaxa_apply
A class for multiple taxon objects	taxa
Taxmap class	taxmap
Taxon class	taxon
Taxonomy database class	taxon_database
Taxon ID class	taxon_id
Get taxon IDs	taxon_ids
Get taxon indexes	taxon_indexes
Taxon name class	taxon_name
Get taxon names	taxon_names
Taxon rank class	taxon_rank
Get taxon ranks	taxon_ranks
Taxonomy class	taxonomy
Convert taxonomy info to a table	taxonomy_table
Replace columns in [taxmap()] objects	transmute_obs
Write an imitation of the Greengenes database	write_greengenes
Write an imitation of the Mothur taxonomy file	write_mothur_taxonomy
Write an imitation of the RDP FASTA database	write_rdp
Write an imitation of the SILVA FASTA database	write_silva_fasta
Write an imitation of the UNITE general FASTA database	write_unite_general
Replace low counts with zero	zero_low_counts