Package 'refdb'

Title: A DNA Reference Library Manager
Description: Reference database manager offering a set of functions to import, organize, clean, filter, audit and export reference genetic data. Provide functions to download sequence data from NCBI GenBank <https://www.ncbi.nlm.nih.gov/genbank/>. Designed as an environment for semi-automatic and assisted construction of reference databases and to improve standardization and repeatability in barcoding and metabarcoding studies.
Authors: Francois Keck [aut, cre, cph] (ORCID: <https://orcid.org/0000-0002-3323-4167>)
Maintainer: Francois Keck <[email protected]>
License: GPL-3
Version: 0.1.3
Built: 2026-05-28 07:02:40 UTC
Source: https://github.com/fkeck/refdb

Help Index

Internal check for fields

Description

Internal check for fields

Usage

check_fields(x, what = c("source", "id", "taxonomy", "sequence", "marker"))

Arguments

x

a reference database (tibble object).
what

a vector of fields to be checked.

Value

Invisible or error.

Functions to set fields for various databases

Description

Functions to set fields for various databases

Usage

refdb_set_fields_NCBI(x)

refdb_set_fields_BOLD(x)

refdb_set_fields_PR2(x)

refdb_set_fields_diatbarcode(x)

Arguments

x

a reference database.

Value

The function returns x with updated attributes.

Examples

lib <- read.csv(system.file("extdata", "baetidae_bold.csv", package = "refdb"))
refdb_set_fields_BOLD(lib)

Scores for filtering operations

Description

Scores for filtering operations

Usage

.filter_seq_length(x, gaps)

Arguments

x

a reference database
gaps

should gaps be included.

Value

a numeric vector

Get NCBI taxonomy

Description

Download and parse NCBI taxonomy records

Usage

get_ncbi_taxonomy(id, verbose = TRUE)

Arguments

id

A vector of id for records in the NCBI Taxonomy database.
verbose

print information in the console.

Value

A tibble with each row corresponding to an id and each column to a taxonomic level.

Create a graph from a taxonomic table

Description

Create a graph representation from a taxonomic classification included in a reference database. For this function to work, taxonomic fields must be set.

Usage

igraph_from_taxo(x, cols = NULL)

Arguments

x

a reference database (tibble).
cols

an optional vector of column names to use a subset of columns.

Value

An igraph object representing taxonomic relationships.

Parse NCBI XML and make a table

Description

Parse NCBI XML and make a table

Usage

make_ncbi_table(x)

Arguments

x

A XML nodeset.

Value

A tibble.

Taxonomic ranks of the NCBI Taxonomy database

Description

Taxonomic ranks of the NCBI Taxonomy database

Usage

ncbi_taxo_rank()

Value

a vector of ordered ranks

Process coordinate column returned by NCBI

Description

Process coordinate column returned by NCBI

Usage

process_geo_ncbi(x, col = "lat_lon")

Arguments

x

NCBI dataframe.
col

column name containing geographical coordinates.

Value

NCBI dataframe.

Check for conflicts in sequences

Description

Check for conflicts in sequences

Usage

refdb_check_seq_conflict(x, na_omit = TRUE)

Arguments

x

a reference database.
na_omit

if FALSE conflicts involving NA taxonomic names are also reported.

Value

A list of two-columns tibbles reporting duplicated sequences with different taxonomy.

Examples

lib <- read.csv(system.file("extdata", "ephem.csv", package = "refdb"))
lib <- refdb_set_fields(lib,
                        taxonomy = c(family = "family_name",
                            genus = "genus_name",
                            species = "species_name"),
                        sequence = "DNA_seq",
                        marker = "marker")
refdb_check_seq_conflict(lib)

Check for genetic homogeneity of taxa

Description

This function assesses the genetic similarity among sequences within each taxa. It takes user defined thresholds (one threshold per taxonomic level) to warn about sequences which are singularly different (based on median distance) from the others. Sequences in the reference database must be aligned.

Usage

refdb_check_seq_homogeneity(x, levels, min_n_seq = 3)

Arguments

x

a reference database (sequences must be aligned).
levels

a named vector of genetic similarity thresholds. Names must correspond to taxonomic levels (taxonomic fields) and values must be included in the interval [0, 1]. For example to assess homogeneity at 5 percents (within species) and 10 percents (within genus): levels = c(species = 0.05, genus = 0.1)
min_n_seq

the minimum number of sequences for a taxon to be tested.

Details

For every tested taxonomic levels, the algorithm checks all sequences in every taxa (for which the total number of sequence is > min_n_seq) In each taxon, the pairwise distance matrix among all the sequences belonging to this taxon is computed. A sequence is tagged as suspicious and returned by the function if its median genetic distance from the other sequences is higher than the threshold set by the user (levels argument).

Value

A dataframe reporting suspicious sequences whose median distance to other sequences of the same taxon is greater than the specified threshold. The first column "level_threshold_homogeneity" indicates the lowest taxonomic level for which the threshold has been exceeded and the second column "value_threshold_homogeneity" gives the computed median distance.

Examples

lib <- read.csv(system.file("extdata", "homogeneity.csv", package = "refdb"))
lib <- refdb_set_fields_BOLD(lib)
refdb_check_seq_homogeneity(lib, levels = c(species = 0.05, genus = 0.1))

Check for conflicts in taxonomy

Description

Check for conflicts in taxonomy

Usage

refdb_check_tax_conflict(x)

Arguments

x

a reference database.

Value

A list of two-columns tibbles reporting for each taxonomic level the taxa with identical names but different upstream taxonomy.

Examples

lib <- read.csv(system.file("extdata", "ephem.csv", package = "refdb"))
lib <- refdb_set_fields(lib,
                        taxonomy = c(family = "family_name",
                            genus = "genus_name",
                            species = "species_name"),
                        sequence = "DNA_seq",
                        marker = "marker")
refdb_check_tax_conflict(lib)

Check for typos in taxonomic names

Description

This function uses the generalized Levenshtein (edit) distance to identify possible issue with taxonomic names.

Usage

refdb_check_tax_typo(x, tol = 1)

Arguments

x

a reference database.
tol

the edit distance below which two taxonomic names are reported.

Value

A list of two-columns tibbles reporting for each taxonomic level the pairs of taxonomic names sharing the same upstream taxonomy and for which the generalized Levenshtein (edit) distance is below the tol value.

Examples

lib <- read.csv(system.file("extdata", "ephem.csv", package = "refdb"))
lib <- refdb_set_fields(lib,
                        taxonomy = c(family = "family_name",
                            genus = "genus_name",
                            species = "species_name"),
                        sequence = "DNA_seq",
                        marker = "marker")
refdb_check_tax_typo(lib)

Crop genetic sequences with a set of primers

Description

Crop genetic sequences with a set of primers

Usage

refdb_clean_seq_crop_primers(
  x,
  primer_forward,
  primer_reverse,
  max_error_in = 0.1,
  max_error_out = 0.1,
  include_primers = TRUE
)

Arguments

x

a reference database with a defined sequence field.
primer_forward

primer forward.
primer_reverse

primer reverse.
max_error_in, max_error_out

maximum error for a match (frequency based on primer length).
include_primers

a logical indicating whether the detected primers are included in the cropped sequences.

Value

A reference database.

Examples

lib <- read.csv(system.file("extdata", "baetidae_bold.csv", package = "refdb"))
lib <- refdb_set_fields_BOLD(lib)
refdb_clean_seq_crop_primers(lib, "AGT", "TTTA")

Remove gaps from genetic sequences

Description

Remove gaps from genetic sequences

Usage

refdb_clean_seq_remove_gaps(x)

Arguments

x

a reference database with a defined sequence field.

Value

A reference database.

Examples

lib <- read.csv(system.file("extdata", "baetidae_bold.csv", package = "refdb"))
lib <- refdb_set_fields_BOLD(lib)
refdb_clean_seq_remove_gaps(lib)

Remove repeated side N from genetic sequences

Description

Remove repeated side N from genetic sequences

Usage

refdb_clean_seq_remove_sideN(x, side = "both")

Arguments

x

a reference database with a defined sequence field.
side

which side to clean. Can be one of "left", "right" or "both" (default).

Value

A reference database.

Examples

lib <- read.csv(system.file("extdata", "baetidae_bold.csv", package = "refdb"))
lib <- refdb_set_fields_BOLD(lib)
refdb_clean_seq_remove_sideN(lib)

Harmonize taxonomic name nomenclature

Description

Harmonize taxonomic name nomenclature

Usage

refdb_clean_tax_harmonize_nomenclature(x, cols = NULL)

Arguments

x

a reference database.
cols

an optional vector of column names. If NULL (default), the function is applied to the columns associated with the taxonomy and organism fields.

Value

A reference database.

Examples

lib <- read.csv(system.file("extdata", "baetidae_bold.csv", package = "refdb"))
lib <- refdb_set_fields_BOLD(lib)
refdb_clean_tax_harmonize_nomenclature(lib)

Convert missing taxonomic names to NA

Description

Convert missing taxonomic names to NA

Usage

refdb_clean_tax_NA(x, cols = NULL, hybrid = TRUE, uncertain = FALSE)

Arguments

x

a reference database.
cols

an optional vector of column names. If NULL (default), the function is applied to the columns associated with the taxonomy and organism fields.
hybrid

hybrids are converted to NA (default TRUE).
uncertain

taxa with qualifiers of uncertainty (cf., aff., etc.) are converted to NA (default FALSE).

Value

A reference database.

Examples

lib <- read.csv(system.file("extdata", "baetidae_bold.csv", package = "refdb"))
lib <- refdb_set_fields_BOLD(lib)
refdb_clean_tax_NA(lib)

Remove blank characters from taxonomic names

Description

Remove blank characters from taxonomic names

Usage

refdb_clean_tax_remove_blank(x, cols = NULL)

Arguments

x

a reference database.
cols

an optional vector of column names. If NULL (default), the function is applied to the columns associated with the taxonomy and organism fields.

Value

A reference database.

Examples

lib <- read.csv(system.file("extdata", "baetidae_bold.csv", package = "refdb"))
lib <- refdb_set_fields_BOLD(lib)
refdb_clean_tax_remove_blank(lib)

Remove extra words from taxonomic names

Description

Remove extra words from taxonomic names

Usage

refdb_clean_tax_remove_extra(x, cols = NULL)

Arguments

x

a reference database.
cols

an optional vector of column names. If NULL (default), the function is applied to the columns associated with the taxonomy and organism fields.

Details

As the function can match words like "g.", "s." or "x", which can have a signification in some nomenclatures, it is recommended to execute refdb_clean_tax_harmonize_nomenclature first.

Value

A reference database.

lib <- read.csv(system.file("extdata", "baetidae_bold.csv", package = "refdb")) lib <- refdb_set_fields_BOLD(lib) refdb_clean_tax_remove_extra(lib)

Remove subspecific information from taxonomic names

Description

Remove subspecific information from taxonomic names

Usage

refdb_clean_tax_remove_subsp(x, cols = NULL)

Arguments

x

a reference database.
cols

an optional vector of column names. If NULL (default), the function is applied to the columns associated with the taxonomy and organism fields.

Value

A reference database.

Examples

lib <- read.csv(system.file("extdata", "baetidae_bold.csv", package = "refdb"))
lib <- refdb_set_fields_BOLD(lib)
refdb_clean_tax_remove_subsp(lib)

Remove terms indicating uncertainty in taxonomic names

Description

Remove terms indicating uncertainty in taxonomic names

Usage

refdb_clean_tax_remove_uncertainty(x, cols = NULL)

Arguments

x

a reference database.
cols

an optional vector of column names. If NULL (default), the function is applied to the columns associated with the taxonomy and organism fields.

Value

A reference database.

Warning

Marks of taxonomic uncertainty provided by specialists are not without value. The consequences of their deletion must be well understood by the user before using this function.

Examples

lib <- read.csv(system.file("extdata", "baetidae_bold.csv", package = "refdb"))
lib <- refdb_set_fields_BOLD(lib)
refdb_clean_tax_remove_uncertainty(lib)

Export reference database for DADA2

Description

Write reference database in formats which can be used with the functions of the package dada2.

Usage

refdb_export_dada2(x, file, mode = "taxonomy")

Arguments

x

a reference database.
file

a path to the file to be written.
mode

character string to determine the type of file to produce. Use "taxonomy" to produce a file for function assignTaxonomy or "species" to produce a file for function assignSpecies.

Value

No return value, called for side effects.

Examples

lib <- read.csv(system.file("extdata", "baetidae_bold.csv", package = "refdb"))
lib <- refdb_set_fields_BOLD(lib)
refdb_export_dada2(lib, tempfile())

Export reference database for DECIPHER (IDTAXA)

Description

Write a reference database in file formats which can be used to train the IDTAXA classifier implemented in DECIPHER.

Usage

refdb_export_idtaxa(x, file, taxid = FALSE)

Arguments

x

a reference database.
file

a file path without extension. This will be used to create a .fasta file and two .txt files.
taxid

should the taxid file be generated (can be very slow with large databases)

Details

The functions generates three files.

- A fasta files containing the sequences with their IDs. This file must be imported as a DNAStringSet to be used with DECIPHER, using eg:
Biostrings::readDNAStringSet("ex_seqs.fasta")

- A text files containing the sequence taxonomic assignment. This file must be imported as a character vector to be used with DECIPHER, using eg:
readr::read_lines("ex_taxo.txt")

- A text file ("taxid") containing the taxonomic ranks associated with each taxon. This is an asterisk delimited file which must be imported as a dataframe (see LearnTaxa), using eg:
readr::read_delim("ex_ranks.txt", col_names = c('Index', 'Name', 'Parent', 'Level', 'Rank'), delim = "*", quote = "")

The taxid file can be very slow to write for large datasets. Therefore it is not generated by default.

Value

No return value, called for side effects.

Examples

lib <- read.csv(system.file("extdata", "baetidae_bold.csv", package = "refdb"))
lib <- refdb_set_fields_BOLD(lib)
refdb_export_idtaxa(lib, tempfile())

Export reference database for Mothur

Description

Write a reference database in formats which can be used with Mothur.

Usage

refdb_export_mothur(x, file)

Arguments

x

a reference database.
file

a file path. This will be used to create a .fasta file and a .txt file.

Value

No return value, called for side effects.

Examples

lib <- read.csv(system.file("extdata", "baetidae_bold.csv", package = "refdb"))
lib <- refdb_set_fields_BOLD(lib)
refdb_export_mothur(lib, tempfile())

Export reference database for USEARCH/VSEARCH

Description

Write a reference database in utax format.

Usage

refdb_export_utax(x, file, verbose = TRUE)

Arguments

x

a reference database.
file

a file path. This will be used to create a .fasta file.
verbose

print information in the console.

Value

No return value, called for side effects.

Examples

lib <- read.csv(system.file("extdata", "baetidae_bold.csv", package = "refdb"))
lib <- refdb_set_fields_BOLD(lib)
refdb_export_utax(lib, tempfile())

Fill missing data in taxonomy

Description

Replace NA values in taxonomic classification using upstream ranks.

Usage

refdb_fill_tax_downstream(x, qualifier = "indet.")

Arguments

x

a reference database.
qualifier

a string to add the new labels. Default ensure that refdb_clean_tax_NA will correctly identify the label as NA.

Value

A reference database.

See Also

refdb_fill_tax_upstream to replace NA values using downstream data.

Examples

lib <- read.csv(system.file("extdata", "baetidae_bold.csv", package = "refdb"))
lib <- refdb_set_fields_BOLD(lib)
refdb_fill_tax_downstream(lib)

Fill missing data in taxonomy

Description

Replace NA values in taxonomic classification using downstream ranks.

Usage

refdb_fill_tax_upstream(x, qualifier = "undef.")

Arguments

x

a reference database.
qualifier

a string to add the new labels. Default ensure that refdb_clean_tax_NA will correctly identify the label as NA.

Value

A reference database.

See Also

refdb_fill_tax_downstream to replace terminal NA values using upstream data.

Examples

lib <- read.csv(system.file("extdata", "baetidae_bold.csv", package = "refdb"))
lib <- refdb_set_fields_BOLD(lib)
refdb_fill_tax_upstream(lib)

Filter records by taxonomic scope of studies

Description

Filter records by taxonomic scope of studies

Usage

refdb_filter_ref_scope(x, max_tax)

Arguments

x

a reference database (tibble).
max_tax

the maximum (widest) taxonomic focus of the study.

Details

A reference field (one ore more columns) must be set to use this function. If reference is not available (NA) for a record, the record is not dropped.

Value

a reference database (tibble).

Examples

lib <- read.csv(system.file("extdata", "baetidae_bold.csv", package = "refdb"))
lib <- refdb_set_fields_BOLD(lib)
lib$refs <- rep("REF_1", nrow(lib))
lib <- refdb_set_fields(lib, reference = "refs")
refdb_filter_ref_scope(lib, max_tax = "family_name")

Filter sequences based on their number of ambiguous character.

Description

Filter sequences based on their number of ambiguous character.

Usage

refdb_filter_seq_ambiguous(x, max_ambig = 3L, char = "N")

Arguments

x

a reference database.
max_ambig

maximum number of ambiguous character.
char

characters interpreted as ambiguous (vector).

Value

A tibble (filtered reference database).

Examples

lib <- read.csv(system.file("extdata", "baetidae_bold.csv", package = "refdb"))
lib <- refdb_set_fields_BOLD(lib)
refdb_filter_seq_ambiguous(lib)

Filter duplicated sequences.

Description

Exclude duplicated sequences. This is based both on sequences and taxonomy. NA values are assumed to be comparable.

Usage

refdb_filter_seq_duplicates(x)

Arguments

x

a reference database.

Value

A tibble (filtered reference database).

Examples

lib <- read.csv(system.file("extdata", "baetidae_bold.csv", package = "refdb"))
lib <- refdb_set_fields_BOLD(lib)
refdb_filter_seq_duplicates(lib)

Filter sequences based on their number of repeated character.

Description

Filter sequences based on their number of repeated character.

Usage

refdb_filter_seq_homopolymers(x, max_len = 16L)

Arguments

x

a reference database.
max_len

maximum number of repeated character (homopolymer).

Value

A tibble (filtered reference database).

Examples

lib <- read.csv(system.file("extdata", "baetidae_bold.csv", package = "refdb"))
lib <- refdb_set_fields_BOLD(lib)
refdb_filter_seq_homopolymers(lib)

Filter sequences based on their number of character.

Description

Filter sequences based on their number of character.

Usage

refdb_filter_seq_length(x, min_len = NULL, max_len = NULL, gaps = FALSE)

Arguments

x

a reference database.
min_len, max_len

minimum and maximum sequence lengths. Use NULL (default) to ignore.
gaps

if TRUE gaps are accounted.

Value

A tibble (filtered reference database).

Examples

lib <- read.csv(system.file("extdata", "baetidae_bold.csv", package = "refdb"))
lib <- refdb_set_fields_BOLD(lib)
refdb_filter_seq_length(lib, 50L)

Filter sequences based on the presence of primers.

Description

Filter sequences based on the presence of primers.

Usage

refdb_filter_seq_primer(
  x,
  primer_forward = NULL,
  primer_reverse = NULL,
  max_error_forward = 0.1,
  max_error_reverse = 0.1
)

Arguments

x

a reference database.
primer_forward

forward primer.
primer_reverse

reverse primer.
max_error_forward, max_error_reverse

maximum error for match (frequency base on primer length).

Value

A tibble (filtered reference database).

Examples

lib <- read.csv(system.file("extdata", "baetidae_bold.csv", package = "refdb"))
lib <- refdb_set_fields_BOLD(lib)
refdb_filter_seq_primer(lib, "ACTA")

Filter sequences based on their number of of stop codons.

Description

Filter sequences based on their number of of stop codons.

Usage

refdb_filter_seq_stopcodon(x, max_stop = 0, code, codon_frame = NA)

Arguments

x

a reference database.
max_stop

maximum number of stop codons.
code

an integer indicating the genetic code to use for translation (see genetic-codes).
codon_frame

an integer giving the nucleotide position where to start translation. If NA (the default), the three different frames are tested and the frame producing the lowest number of stop codons will be used.

Value

A tibble (filtered reference database).

Examples

lib <- read.csv(system.file("extdata", "baetidae_bold.csv", package = "refdb"))
lib <- refdb_set_fields_BOLD(lib)
refdb_filter_seq_stopcodon(lib, code = 5)

Filter records NA taxa

Description

Remove records where taxa is NA if it is not the only representant of the upper clade. Note that the function maybe slow on large datasets. //EXPERIMENTAL//

Usage

refdb_filter_tax_na(x)

Arguments

x

a reference database. (column name of the reference database).

Value

A tibble (filtered reference database).

Examples

lib <- read.csv(system.file("extdata", "baetidae_bold.csv", package = "refdb"))
lib <- refdb_set_fields_BOLD(lib)
refdb_filter_tax_na(lib)

Filter records based on their taxonomic precision.

Description

Filter records based on their taxonomic precision.

Usage

refdb_filter_tax_precision(x, min_tax)

Arguments

x

a reference database.
min_tax

minimum taxonomic level (column name of the reference database).

Value

A tibble (filtered reference database).

Examples

lib <- read.csv(system.file("extdata", "baetidae_bold.csv", package = "refdb"))
lib <- refdb_set_fields_BOLD(lib)
refdb_filter_tax_precision(lib, min_tax = "family_name")

Get fields of a reference database

Description

Get fields of a reference database

Usage

refdb_get_fields(x, silent = FALSE)

Arguments

x

a reference database.
silent

if TRUE silently and invisibly returns fields.

Value

The list of fields is returned invisibly.

Examples

lib <- read.csv(system.file("extdata", "ephem.csv", package = "refdb"))
refdb_get_fields(lib)

Download and import NCBI Nucleotide records

Description

This function allows to search and download data from the the NCBI Nucleotide database. Additionally it uses the NCBI Taxonomy database to get the sequence taxonomic classification.

Usage

refdb_import_NCBI(
  query,
  full = FALSE,
  max_seq_length = 10000,
  seq_bin = 200,
  verbose = TRUE,
  start = 0L
)

Arguments

query

a character string with the query.
full

a logical. If FALSE (the default), only a subset of the most important fields is included in the result.
max_seq_length

a numeric giving the maximum length of sequences to retrieve. Useful to exclude complete genomes.
seq_bin

number of sequences to download at once.
verbose

print information in the console.
start

an integer giving the index where to start to download. For debugging purpose mainly.

Details

This function uses several functions of the rentrez package to interface with the NCBI's EUtils API.*

Value

A tibble.

Errors

Error in curl::curl_fetch_memory(url, handle = handle) : transfer closed with outstanding read data remaining
This error seems to appear with long sequences. You can try to decrease max_seq_length to exclude them.

Examples

try(silo_ncbi <- refdb_import_NCBI("Silo COI"))

Merge reference databases

Description

Merge several reference database by common fields.

Usage

refdb_merge(..., keep = "fields_all")

Arguments

...

reference databases (tibbles).
keep

determines which columns to keep. Can be "fields_all" (default), "fields_shared" or "all" (see Details).

Details

Columns are merged only if they are associated to the same field.

The keep argument determines which columns are returned as follow. "fields_all" (the default) returns all the fields existing in all the reference databases. "fields_shared" returns only the fields shared by all the reference databases. "all" returns all the columns of all the databases. Columns which are not associated to a field are not merged and are prefixed with the name of the object they originated from.

Value

a merged reference database (tibble).

Examples

lib_1 <- read.csv(system.file("extdata", "baetidae_bold.csv", package = "refdb"))
lib_1 <- refdb_set_fields_BOLD(lib_1)
lib_2 <- lib_1
refdb_merge(lib_1, lib_2)

Plot an interactive map

Description

This functions generate an interactive maps showing the location of the records of a reference database. Note that only records with latitude and longitude data will be displayed.

Usage

refdb_plot_map(x)

Arguments

x

a reference database.

Value

An interactive map object from the leaflet package.

Examples

lib <- read.csv(system.file("extdata", "baetidae_bold.csv", package = "refdb"))
lib <- refdb_set_fields_BOLD(lib)
lib <- refdb_set_fields(lib, latitude = "lat", longitude = "lon")
refdb_plot_map(lib)

Plot an histogram of sequence lengths

Description

Plot an histogram of sequence lengths

Usage

refdb_plot_seqlen_hist(x, remove_gaps = TRUE)

Arguments

x

a reference database
remove_gaps

a logical (default TRUE to control whether gaps (-) should be removed prior computing sequence lengths.

Value

A ggplot object. This means the plot can be further customized using ggplot2 compatible functions.

Examples

lib <- read.csv(system.file("extdata", "baetidae_bold.csv", package = "refdb"))
lib <- refdb_set_fields_BOLD(lib)
refdb_plot_seqlen_hist(lib)

Barplots of the number of records for the most represented taxa

Description

Generate a multipanel plot where, for each taxonomic level, a barplot represent the number of records available in the reference database for the most represented taxa.

Usage

refdb_plot_tax_barplot(x, show_n = 10)

Arguments

x

a reference database.
show_n

an integer value indicating the number of taxa to show in each panel.

Value

A ggplot object.

Examples

lib <- read.csv(system.file("extdata", "baetidae_bold.csv", package = "refdb"))
lib <- refdb_set_fields_BOLD(lib)
lib <- refdb_set_fields(lib, latitude = "lat", longitude = "lon")
refdb_plot_tax_barplot(lib)

Reference database taxonomy tree

Description

Represent the hierarchical structure of the taxonomic information of a reference database as a tree.

Usage

refdb_plot_tax_tree(
  x,
  leaf_col = NULL,
  color_col = NULL,
  freq_labels = 0,
  expand_plot = 0.5
)

Arguments

x

a reference database.
leaf_col

a column name referring to the taxonomic level for the leaves of the tree. If not provided (NULL) the function tries to find a relevant level.
color_col

a column name referring to the taxonomic level for the color of the leaves (must be higher or equal to the level of leaf_col). If not provided (NULL) the function tries to find a relevant level.
freq_labels

a numeric value to adjust the number of printed labels (minimum frequency). Default is zero which means all non-NA labels are printed.
expand_plot

a value to expand the limits of the plot. Useful if the labels are too long.

Details

The underlying graph is computed using the non-exported function igraph_from_taxo.

Value

A ggplot2 (ggraph) object. This means the plot can be further customized using ggplot2 compatible functions.

Examples

lib <- read.csv(system.file("extdata", "baetidae_bold.csv", package = "refdb"))
lib <- refdb_set_fields_BOLD(lib)
refdb_plot_tax_tree(lib)

Reference database treemap

Description

Represent the hierarchical structure of the taxonomic information of a reference database as a set of nested rectangles (treemap).

Usage

refdb_plot_tax_treemap(x, cols = NULL, freq_labels = c(0.01, 0.003))

Arguments

x

a reference database.
cols

a vector of column names referring to taxonomic levels to include in the treemap. If not provided (NULL) the function tries to find a relevant subset of columns.
freq_labels

a numeric vector of length two to adjust the number of printed labels (see Details).

Only the columns provided in the cols argument are represented in the treemap. Large labels are printed for the highest rank, while light text labels are printed for the lowest rank Intermediate ranks are drawn but their names are not shown.

The number of labels printed are determined by freq_labels. The first value gives the threshold for the highest rank (large labels) and the second value gives the threshold for the lowest rank (light text labels).

The underlying graph is computed using the non-exported function igraph_from_taxo.

Value

A ggplot2 (ggraph) object. This means the plot can be further customized using ggplot2 compatible functions.

Examples

lib <- read.csv(system.file("extdata", "baetidae_bold.csv", package = "refdb"))
lib <- refdb_set_fields_BOLD(lib)
refdb_plot_tax_treemap(lib)

Compile a report with different checks

Description

This function produce an HTML report to investigate potential issues in a reference database.

Usage

refdb_report(x, file = NULL, view = TRUE)

Arguments

x

a reference database.
file

the file (path) to write the report. If NULL the report is written in the user temp directory.
view

A logical. If TRUE (default), the file is instantly opened in the web browser.

Value

The function invisibly returns the file where the report was written.

Examples

lib <- read.csv(system.file("extdata", "ephem.csv", package = "refdb"))
lib <- refdb_set_fields(lib,
                        taxonomy = c(family = "family_name",
                            genus = "genus_name",
                            species = "species_name"),
                        sequence = "DNA_seq",
                        marker = "marker")
tmp <- tempfile()

refdb_report(lib, tmp, view = FALSE)

Sample records within taxa

Description

This function can be useful to keep a maximum of records per taxa. This function require dplyr dev version to work because of slice_sample. Will be exported once available.

Usage

refdb_sample_tax(x, n_max = 10, cols = NULL)

Arguments

x

a reference database.
n_max

maximum number of records to keep for each taxa.
cols

an optional vector of column names. If NULL (default), the function is applied to the columns associated with the taxonomy field.

Value

A reference database.

Associate columns to fields

Description

Associate columns to fields so they are recognized and appropriately treated by refdb functions.

Usage

refdb_set_fields(
  x,
  source = NA,
  id = NA,
  organism = NA,
  taxonomy = NA,
  sequence = NA,
  marker = NA,
  latitude = NA,
  longitude = NA,
  reference = NA,
  config_yaml = NULL
)

Arguments

x

a reference database (tibble).
source

name of the column which contains the data source.
id

name of the column which contains the record IDs.
organism

name of the column which contains the names of the organisms.
taxonomy

a vector of column names.
sequence

name of the column which contains the sequences.
marker

name of the column which contains marker names.
latitude

name of the column which contains latitudes (WGS 84)
longitude

name of the column which contains longitudes (WGS 84).
reference

a vector of column names.
config_yaml

a file path to a YAML file

Details

Taxonomy reordering. NA to ignore, NULL to delete. Fields set using config_yaml always overwrite those set by arguments

Value

The function returns x with updated attributes.

Examples

lib <- read.csv(system.file("extdata", "ephem.csv", package = "refdb"))
lib <- refdb_set_fields(lib,
                        taxonomy = c(family = "family_name",
                            genus = "genus_name",
                            species = "species_name"),
                        sequence = "DNA_seq",
                        marker = "marker")

Replace the current taxonomy using the NCBI Taxonomy database

Description

Replace the current taxonomy using the NCBI Taxonomy database

Usage

refdb_set_ncbitax(
  x,
  min_level = "species",
  force_species_name = TRUE,
  verbose = TRUE
)

Arguments

x

a reference database (tibble) with one or several columns giving the taxonomy of each record and explicitly indicated in the field taxonomy. See refdb_set_fields.
min_level

minimum taxonomic level at which taxonomy should be replaced. Default is the finest level ("species").
force_species_name

if TRUE, species not found in NCBI Taxonomy will keep their original names instead of NAs.
verbose

print information in the console.

Value

The reference database with the NCBI taxonomy for the genus level and higher ranks. (the original taxonomy above the genus level is removed).

Examples

lib <- read.csv(system.file("extdata", "baetidae_bold.csv", package = "refdb"))
lib <- refdb_set_fields_BOLD(lib)
try(refdb_set_ncbitax(lib))

Write fields to a file

Description

This function can be used to save fields defined using e.g. refdb_set_fields to a file. Data are saved in YAML and can be read again using the config_yaml argument of refdb_set_fields.

Usage

refdb_write_fields(x, file)

Arguments

x

a reference database with some fields to be saved.
file

a path to the file to write.

Value

No return value, called for its side effects.

Examples

lib <- read.csv(system.file("extdata", "ephem.csv", package = "refdb"))
tmp <- tempfile()
refdb_write_fields(lib, tmp)

Ranks considered as valid by refdb

Description

Ranks considered as valid by refdb

Usage

valid_taxo_rank()

Value

a vector of ordered ranks.

References

This is a simplified version of the list rank_ref available in taxize.

Examples

valid_taxo_rank()

Extract XML elements

Description

Combine xml_find_first and xml_text to extract elements.

Usage

xml_extract(x, xpath)

Arguments

x

A document, node, or node set.
xpath

A string containing a xpath expression.

Value

A character vector, the same length as x.