Read phyloseq object from multiple csv tables and a phylogenetic tree in Newick format.

Usage

read_pq(
  path = NULL,
  taxa_are_rows = FALSE,
  sam_names = NULL,
  sep_csv = "\t",
  ...
)

Arguments

path: (required) a path to the folder to read the phyloseq object
taxa_are_rows: (default to FALSE) see ?phyloseq for details
sam_names: The name of the variable (column) in sam_data.csv to rename samples. Note that if you use write_phyloseq() function to save your physeq object, you may use sam_names = "X" to rename the samples names as before.
sep_csv: (default tabulation) separator for column
...: Other arguments passed on to utils::write.table() function.

Value

One to four csv tables (refseq.csv, otu_table.csv, tax_table.csv, sam_data.csv) and if present a phy_tree in Newick format. At least the otu_table.csv need to be present.

Examples

write_pq(data_fungi, path = paste0(tempdir(), "/phyloseq"))
#> Cleaning suppress 0 taxa and 0 samples.
read_pq(path = paste0(tempdir(), "/phyloseq"))
#> phyloseq-class experiment-level object
#> otu_table()   OTU Table:         [ 1420 taxa and 185 samples ]
#> sample_data() Sample Data:       [ 185 samples by 8 sample variables ]
#> tax_table()   Taxonomy Table:    [ 1420 taxa by 12 taxonomic ranks ]
#> refseq()      DNAStringSet:      [ 1420 reference sequences ]
unlink(paste0(tempdir(), "/phyloseq"), recursive = TRUE)