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Assign Taxonomy using Sintax algorithm of Vsearch

Source: R/vsearch.R
assign_sintax.Rd

lifecycle-experimental

Please cite Vsearch if you use this function to assign taxonomy.

Usage

assign_sintax(
  physeq = NULL,
  seq2search = NULL,
  ref_fasta = NULL,
  behavior = "return_matrix",
  vsearchpath = "vsearch",
  clean_pq = TRUE,
  nproc = 1,
  suffix = "",
  taxo_rank = c("K", "P", "C", "O", "F", "G", "S"),
  min_boostrap = 0.5,
  keep_temporary_files = FALSE,
  verbose = TRUE,
  temporary_fasta_file = "temp.fasta",
  cmd_args = "--sintax_random"
)

Arguments

physeq

(required): a phyloseq-class object obtained using the phyloseq package.

A DNAStringSet object of sequences to search for.

ref_fasta

(required) A link to a database in vsearch format The reference database must contain taxonomic information in the header of each sequence in the form of a string starting with ";tax=" and followed by a comma-separated list of up to nine taxonomic identifiers. Each taxonomic identifier must start with an indication of the rank by one of the letters d (for domain) k (kingdom), p (phylum), c (class), o (order), f (family), g (genus), s (species), or t (strain). The letter is followed by a colon (:) and the name of that rank. Commas and semicolons are not allowed in the name of the rank. Non-ascii characters should be avoided in the names.

Example:

\>X80725_S000004313;tax=d:Bacteria,p:Proteobacteria,c:Gammaproteobacteria,o:Enterobacteriales,f:Enterobacteriaceae,g:Escherichia/Shigella,s:Escherichia_coli,t:str._K-12_substr._MG1655

behavior

Either "return_matrix" (default), "return_cmd", or "add_to_phyloseq":

  • "return_matrix" return a list of two matrix with taxonomic value in the first element of the list and bootstrap value in the second one.

  • "return_cmd" return the command to run without running it.

  • "add_to_phyloseq" return a phyloseq object with amended slot @taxtable. Only available if using physeq input and not seq2search input.

vsearchpath

(default: "vsearch") path to vsearch

clean_pq

(logical, default TRUE) If set to TRUE, empty samples and empty ASV are discarded before clustering.

nproc

(default: 1) Set to number of cpus/processors to use

suffix

(character) The suffix to name the new columns. If set to "" (the default), the taxo_rank algorithm is used without suffix.

taxo_rank

A list with the name of the taxonomic rank present in ref_fasta

min_boostrap

(Int. [0:1], default 0.5) Minimum bootstrap value to inform taxonomy. For each bootstrap below the min_boostrap value, the taxonomy information is set to NA.

keep_temporary_files

(logical, default: FALSE) Do we keep temporary files?

  • temporary_fasta_file (default "temp.fasta") : the fasta file from physeq or seq2search

  • "output_taxo_vs.txt" : see Vsearch Manual for parameter –tabbedout

verbose

(logical). If TRUE, print additional information.

temporary_fasta_file

The name of a temporary_fasta_file (default "temp.fasta")

cmd_args

Other arguments to be passed on to vsearch sintax cmd. By default cmd_args is equal to "–sintax_random" as recommended by Torognes.

Value

See param behavior

Details

This function is mainly a wrapper of the work of others. Please cite vsearch.

Author

Adrien Taudière

Examples

# \donttest{
assign_sintax(data_fungi_mini,
  ref_fasta = system.file("extdata", "mini_UNITE_fungi.fasta.gz", package = "MiscMetabar"),
  behavior = "return_cmd"
)
#> Cleaning suppress 0 taxa and 0 samples.
#> Start Vsearch sintax
#> [1] "vsearch  --sintax temp.fasta --db /tmp/RtmpbOMt4J/temp_libpath32c49814bbb/MiscMetabar/extdata/mini_UNITE_fungi.fasta.gz --tabbedout output_taxo_vs.txt  --threads 1 --sintax_random"

data_fungi_mini_new <- assign_sintax(data_fungi_mini,
  ref_fasta = system.file("extdata", "mini_UNITE_fungi.fasta.gz", package = "MiscMetabar"),
  behavior = "add_to_phyloseq"
)
#> Cleaning suppress 0 taxa and 0 samples.
#> Start Vsearch sintax

assignation_results <- assign_sintax(data_fungi_mini,
  ref_fasta = system.file("extdata", "mini_UNITE_fungi.fasta.gz", package = "MiscMetabar")
)
#> Cleaning suppress 0 taxa and 0 samples.
#> Start Vsearch sintax

left_join(
  tidyr::pivot_longer(assignation_results$taxo_value, -taxa_names),
  tidyr::pivot_longer(assignation_results$taxo_boostrap, -taxa_names),
  by = join_by(taxa_names, name),
  suffix = c("rank", "bootstrap")
) |>
  mutate(name = factor(name, levels = c("K", "P", "C", "O", "F", "G", "S"))) |>
  # mutate(valuerank = forcats::fct_reorder(valuerank, as.integer(name), .desc = TRUE)) |>
  ggplot(aes(valuebootstrap,
    valuerank,
    fill = name
  )) +
  geom_jitter(alpha = 0.8, aes(color = name)) +
  geom_boxplot(alpha = 0.3)

# }