Importing from phyloseq

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if (!requireNamespace("phyloseq", quietly = TRUE)) {
  message("Suggested package: 'phyloseq' is not installed")
  knitr::opts_chunk$set(eval = FALSE)
} else {
  library(phyloseq)
}
library(strollur)

strollur includes functionality for the reading and writing of phyloseq objects. To convert a phyloseq object to a strollur object, you need to run the read_phyloseq() function.

# Using the phyloseq example data
phylo_object <- readRDS(strollur_example("GlobalPatterns.RDS"))
rdata_object <- read_phyloseq(phylo_object)
#> Added 19216 sequences.
#> Assigned 19216 sequence abundances.
#> Assigned 19216 sequence taxonomies.
#> Added metadata.
rdata_object
#> 
#> Number of unique seqs: 19216 
#> Total number of seqs: 28216678 
#> 
#> Total number of samples: 26 
#> Total number of sequence classifications: 19216 
#> Your dataset includes metadata

Now that are phyloseq object is converted into a strollur object, we can utilize functions like count(), abundance(), and names() to inspect the data.

count(rdata_object, type = "sample")
#> [1] 26
head(names(rdata_object, type = "sequence"))
#> [1] "549322" "522457" "951"    "244423" "586076" "246140"
head(abundance(rdata_object, type = "sequence"))
#>   sequence_name abundance
#> 1        549322       259
#> 2        522457         8
#> 3           951         1
#> 4        244423        51
#> 5        586076         3
#> 6        246140         4

Furthermore, we can output strollur objects as phyloseq objects using the write_phyloseq() function.

phyloseq_object <- write_phyloseq(rdata_object)
phyloseq_object
#> phyloseq-class experiment-level object
#> otu_table()   OTU Table:         [ 19216 taxa and 26 samples ]
#> sample_data() Sample Data:       [ 26 samples by 7 sample variables ]
#> tax_table()   Taxonomy Table:    [ 19216 taxa by 7 taxonomic ranks ]
#> phy_tree()    Phylogenetic Tree: [ 19216 tips and 19215 internal nodes ]


# With the miseq example data
miseq <- miseq_sop_example()
#> Added 2425 sequences.
#> Assigned 2425 sequence abundances.
#> Assigned 2425 sequence taxonomies.
#> Assigned 531 otu bins.
#> Assigned 2425 asv bins.
#> Assigned 63 phylotype bins.
#> Assigned 19 samples to treatments.
#> Assigned 531 otu bin taxonomies.
#> Assigned 531 otu bin representative sequences.
#> Added metadata.
#> Added 2 resource references.
#> Added a contigs_report.
miseq_phyloseq <- write_phyloseq(miseq)
miseq_phyloseq
#> phyloseq-class experiment-level object
#> otu_table()   OTU Table:         [ 2425 taxa and 19 samples ]
#> sample_data() Sample Data:       [ 19 samples by 2 sample variables ]
#> tax_table()   Taxonomy Table:    [ 2425 taxa by 6 taxonomic ranks ]
#> phy_tree()    Phylogenetic Tree: [ 2425 tips and 2424 internal nodes ]

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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