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Build phyloseq objects for all taxonomy ranks

Source: R/build_phyloseq.R
build_phyloseq.Rd

Constructs a list of phyloseq objects from a feature matrix (X), sample data, taxonomy and (optionally) phylogenetic tree data.

Usage

build_phyloseq(
  X,
  sample_data,
  taxa_table = NULL,
  phylo_tree = NULL,
  taxa_in_rows,
  verbose = TRUE
)

Arguments

X

A numeric matrix of NGS features (e.g., ASVs), with samples in rows and features in columns (recommended) or vice versa.

sample_data

A data.frame containing sample data. Row names must match sample identifiers in X.

taxa_table

(Optional) A taxonomy table with row names corresponding to feature names in X, and taxonomic ranks as columns.

phylo_tree

(Optional) A phylogenetic tree.

taxa_in_rows

Logical. If TRUE, X is assumed to have taxa as rows and samples as columns.

verbose

Logical. If TRUE, diagnostic messages will be printed.

Value

A named list of phyloseq objects and related output:

asv

Phyloseq object with the raw feature counts (usually ASVs).

<tax_rank>

Phyloseq objects of higher taxonomy ranks from taxa_table.

Details

Phyloseq objects for higher taxonomic ranks are also generated when taxa_table is provided. Higher rank taxa with labels matching "unclass" or "unknown" are excluded after aggregation.

If very long strings are detected as feature IDs in X matrix or taxa_table, (for example when actual DNA sequence is used as ID), it will issue a warning, as this could significantly slow down computation and increase memory usage.

See also

phyloseq::phyloseq() for further details on phyloseq objects.

Examples

if (requireNamespace("phyloseq", quietly = TRUE)) {
mock_X <- matrix(c(10, 0, 5, 3, 1, 7),
                 nrow = 2, byrow = TRUE,
                 dimnames = list(c("sample1", "sample2"),
                                 c("ASV1", "ASV2", "ASV3"))
                 )

mock_sample_data <- data.frame(sample_id = c("sample1", "sample2"),
                               group = c("A", "B"),
                               row.names = c("sample1", "sample2")
                               )

mock_taxa_table <- data.frame(Domain = c("Bacteria", "Bacteria", "Bacteria"),
                              Genus = c("GenusA", "GenusB", "Unknown"),
                              row.names = c("ASV1", "ASV2", "ASV3")
                              )

phyloseq_ready <- build_phyloseq(X = mock_X,
                                 sample_data = mock_sample_data,
                                 taxa_table = mock_taxa_table,
                                 taxa_in_rows = FALSE,
                                 verbose = FALSE)
}