if (!requireNamespace("phyloseq", quietly = TRUE)) {
message("Suggested package: 'phyloseq' is not installed")
knitr::opts_chunk$set(eval = FALSE)
} else {
library(phyloseq)
}
library(strollur)
#>
#> Attaching package: 'strollur'
#> The following objects are masked from 'package:base':
#>
#> assign, names, summarystrollur includes functionality for the reading and
writing of phyloseq objects. To convert a phyloseq object
to a strollur object, you need to run the
strollur::read_phyloseq() function.
phyloseq_object <- readRDS(strollur_example("GlobalPatterns.RDS"))
class(phyloseq_object)
#> [1] "phyloseq"
#> attr(,"package")
#> [1] "phyloseq"
strollur_object <- strollur::read_phyloseq(phyloseq_object)
#> Added 19216 sequences.
#> Assigned 19216 sequence abundances.
#> Assigned 19216 sequence taxonomies.
#> Added a metadata report.
class(strollur_object)
#> [1] "strollur" "R6"Now that are phyloseq object is converted into a strollur object, we
can utilize functions like strollur::count(),
strollur::abundance(), and strollur::names()
to inspect the data.
strollur::count(strollur_object, type = "sample")
#> [1] 26
head(strollur::names(strollur_object, type = "sequence"))
#> [1] "549322" "522457" "951" "244423" "586076" "246140"
head(strollur::abundance(strollur_object, type = "sequence"))
#> sequence_name abundance
#> 1 549322 259
#> 2 522457 8
#> 3 951 1
#> 4 244423 51
#> 5 586076 3
#> 6 246140 4Furthermore, we can output strollur objects as phyloseq objects using
the strollur::write_phyloseq() function.
phyloseq_object <- strollur::write_phyloseq(strollur_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 ]
miseq <- strollur::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 171 samples distances.
#> Assigned 531 otu bin taxonomies.
#> Assigned 531 otu bin representative sequences.
#> Added a metadata report.
#> Added 2 resource references.
#> Added a contigs_report report.
miseq_phyloseq <- strollur::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 ]