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Clean phyloseq object by removing empty samples and taxa

Source: R/dada_phyloseq.R
clean_pq.Rd

lifecycle-stable

In addition, this function check for discrepancy (and rename) between (i) taxa names in refseq, taxonomy table and otu_table and between (ii) sample names in sam_data and otu_table.

Usage

clean_pq(
  physeq,
  remove_empty_samples = TRUE,
  remove_empty_taxa = TRUE,
  clean_samples_names = TRUE,
  silent = FALSE,
  verbose = FALSE,
  force_taxa_as_columns = FALSE,
  force_taxa_as_rows = FALSE,
  reorder_taxa = FALSE,
  rename_taxa = FALSE,
  simplify_taxo = FALSE,
  prefix_taxa_names = "_Taxa",
  check_taxonomy = FALSE,
  tax_remove_border_spaces = FALSE,
  tax_remove_all_space = FALSE,
  tax_replace_to_NA = FALSE,
  tax_redundant_suffix = FALSE,
  tax_replace_space_with = "_",
  tax_replace_invisible_chars = FALSE,
  tax_replace_NA_string = FALSE
)

Arguments

physeq

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

remove_empty_samples

(logical) Do you want to remove samples without sequences (this is done after removing empty taxa)

remove_empty_taxa

(logical) Do you want to remove taxa without sequences (this is done before removing empty samples)

clean_samples_names

(logical) Do you want to clean samples names?

silent

(logical) If true, no message are printing.

verbose

(logical) Additional informations in the message the verbose parameter overwrite the silent parameter.

force_taxa_as_columns

(logical) If true, if the taxa are rows transpose the otu_table and set taxa_are_rows to false

force_taxa_as_rows

(logical) If true, if the taxa are columns transpose the otu_table and set taxa_are_rows to true

reorder_taxa

(logical) if TRUE the otu_table is ordered by the number of sequences of taxa (ASV, OTU) in descending order. Default to FALSE.

rename_taxa

(logical, default FALSE) if TRUE, taxa (ASV, OTU) are renamed by their position in the OTU_table and prefix_taxa_names param (Taxa_1, Taxa_2, ...). Default to FALSE. If rename taxa (ASV, OTU) is true, the taxa (ASV, OTU) names in verbose information can be misleading.

simplify_taxo

(logical) if TRUE, correct the taxonomy_table using the MiscMetabar::simplify_taxo() function

prefix_taxa_names

(default "Taxa_"): the prefix of taxa names (eg. "ASV_" or "OTU_")

check_taxonomy

(logical, default FALSE) If TRUE, call verify_tax_table() to check for common taxonomy table issues.

tax_remove_border_spaces

(logical, default FALSE) If TRUE, trim leading/trailing whitespace from values in the tax_table slot (passed to verify_tax_table() with modify_phyloseq = TRUE). Handles both ASCII whitespace and Unicode separators such as NBSP (U+00A0).

tax_remove_all_space

(logical, default FALSE) If TRUE, replace internal whitespace (ASCII or Unicode separator) in tax_table values with replace_space_with.

tax_replace_to_NA

(logical or character, default FALSE) If TRUE, replace tax_table values matching the default unwanted_tax_patterns with NA. A character vector of regex patterns can be supplied to override the defaults.

tax_redundant_suffix

(logical or character, default FALSE) If TRUE, replace redundant "_sp" values with NA (e.g. Russula_sp at Species when Russula is already at Genus). A character string supplies a custom suffix.

tax_replace_space_with

(character, default "_") Replacement for internal whitespace when tax_remove_all_space = TRUE.

tax_replace_invisible_chars

(logical, default FALSE) If TRUE, strip invisible / unusual characters (control chars, zero-width space, NBSP inside values, ...) from tax_table values. See verify_tax_table()'s replace_invisible_chars for the exact pattern.

tax_replace_NA_string

(logical, default FALSE) If TRUE, replace the literal strings "NA", "NA NA", "NA NA NA" (any whitespace-separated repetition of NA, a common artifact of pasting taxonomic ranks together) in tax_table values with true <NA>. Case-sensitive to avoid clobbering real data. Default FALSE to avoid breaking changes.

Value

A new phyloseq-class object

Author

Adrien Taudière

Examples

clean_pq(data_fungi_mini)
#> phyloseq-class experiment-level object
#> otu_table()   OTU Table:         [ 45 taxa and 137 samples ]
#> sample_data() Sample Data:       [ 137 samples by 7 sample variables ]
#> tax_table()   Taxonomy Table:    [ 45 taxa by 12 taxonomic ranks ]
#> refseq()      DNAStringSet:      [ 45 reference sequences ]
# \donttest{
# Trim leading/trailing whitespace in tax_table values
clean_pq(data_fungi_mini, tax_remove_border_spaces = TRUE)
#> No values to modify. Returning original phyloseq object.
#> phyloseq-class experiment-level object
#> otu_table()   OTU Table:         [ 45 taxa and 137 samples ]
#> sample_data() Sample Data:       [ 137 samples by 7 sample variables ]
#> tax_table()   Taxonomy Table:    [ 45 taxa by 12 taxonomic ranks ]
#> refseq()      DNAStringSet:      [ 45 reference sequences ]
# Replace NA-like values (e.g. "unidentified", "NA") with NA
clean_pq(data_fungi_mini, tax_replace_to_NA = TRUE)
#> Replaced 4 NA-like value(s) with NA. Unique values: Cantharellales_fam_Incertae_sedis, Atractiellales_fam_Incertae_sedis, Russulales_fam_Incertae_sedis, Hymenochaetales_fam_Incertae_sedis
#> Total: 4 modification(s) in the taxonomy table: 4 value(s) replaced with NA (4 NA-like patterns, 0 short values, 0 redundant suffixes).
#> phyloseq-class experiment-level object
#> otu_table()   OTU Table:         [ 45 taxa and 137 samples ]
#> sample_data() Sample Data:       [ 137 samples by 7 sample variables ]
#> tax_table()   Taxonomy Table:    [ 45 taxa by 12 taxonomic ranks ]
#> refseq()      DNAStringSet:      [ 45 reference sequences ]
# Drop redundant "_sp" tips
clean_pq(data_fungi_mini, tax_redundant_suffix = TRUE)
#> No values to modify. Returning original phyloseq object.
#> phyloseq-class experiment-level object
#> otu_table()   OTU Table:         [ 45 taxa and 137 samples ]
#> sample_data() Sample Data:       [ 137 samples by 7 sample variables ]
#> tax_table()   Taxonomy Table:    [ 45 taxa by 12 taxonomic ranks ]
#> refseq()      DNAStringSet:      [ 45 reference sequences ]
# Replace "NA" / "NA NA" concatenation artifacts with true <NA>
clean_pq(data_fungi_mini, tax_replace_NA_string = TRUE)
#> No values to modify. Returning original phyloseq object.
#> phyloseq-class experiment-level object
#> otu_table()   OTU Table:         [ 45 taxa and 137 samples ]
#> sample_data() Sample Data:       [ 137 samples by 7 sample variables ]
#> tax_table()   Taxonomy Table:    [ 45 taxa by 12 taxonomic ranks ]
#> refseq()      DNAStringSet:      [ 45 reference sequences ]
# }