tests/testthat/_snaps/tax_fix.md

In david-barnett/microViz: Microbiome Data Analysis and Visualization

tax_fix defaults allow agg: enterotype Genus

Code
  tax_agg(ps = fixed, rank = r)
Output
  psExtra object - a phyloseq object with extra slots:

  phyloseq-class experiment-level object
  otu_table()   OTU Table:         [ 553 taxa and 280 samples ]
  sample_data() Sample Data:       [ 280 samples by 9 sample variables ]
  tax_table()   Taxonomy Table:    [ 553 taxa by 1 taxonomic ranks ]

  psExtra info:
  tax_agg = "Genus"

tax_fix defaults allow agg: modified_dietswap Phylum

Code
  tax_agg(ps = fixed, rank = r)
Output
  psExtra object - a phyloseq object with extra slots:

  phyloseq-class experiment-level object
  otu_table()   OTU Table:         [ 12 taxa and 222 samples ]
  sample_data() Sample Data:       [ 222 samples by 8 sample variables ]
  tax_table()   Taxonomy Table:    [ 12 taxa by 1 taxonomic ranks ]

  psExtra info:
  tax_agg = "Phylum"

tax_fix defaults allow agg: modified_dietswap Family

Code
  tax_agg(ps = fixed, rank = r)
Output
  psExtra object - a phyloseq object with extra slots:

  phyloseq-class experiment-level object
  otu_table()   OTU Table:         [ 28 taxa and 222 samples ]
  sample_data() Sample Data:       [ 222 samples by 8 sample variables ]
  tax_table()   Taxonomy Table:    [ 28 taxa by 2 taxonomic ranks ]

  psExtra info:
  tax_agg = "Family"

tax_fix defaults allow agg: modified_dietswap Genus

Code
  tax_agg(ps = fixed, rank = r)
Output
  psExtra object - a phyloseq object with extra slots:

  phyloseq-class experiment-level object
  otu_table()   OTU Table:         [ 110 taxa and 222 samples ]
  sample_data() Sample Data:       [ 222 samples by 8 sample variables ]
  tax_table()   Taxonomy Table:    [ 110 taxa by 3 taxonomic ranks ]

  psExtra info:
  tax_agg = "Genus"

tax_fix defaults allow agg: ibd Kingdom

Code
  tax_agg(ps = fixed, rank = r)
Output
  psExtra object - a phyloseq object with extra slots:

  phyloseq-class experiment-level object
  otu_table()   OTU Table:         [ 1 taxa and 91 samples ]
  sample_data() Sample Data:       [ 91 samples by 15 sample variables ]
  tax_table()   Taxonomy Table:    [ 1 taxa by 1 taxonomic ranks ]

  psExtra info:
  tax_agg = "Kingdom"

tax_fix defaults allow agg: ibd Phylum

Code
  tax_agg(ps = fixed, rank = r)
Output
  psExtra object - a phyloseq object with extra slots:

  phyloseq-class experiment-level object
  otu_table()   OTU Table:         [ 9 taxa and 91 samples ]
  sample_data() Sample Data:       [ 91 samples by 15 sample variables ]
  tax_table()   Taxonomy Table:    [ 9 taxa by 2 taxonomic ranks ]

  psExtra info:
  tax_agg = "Phylum"

tax_fix defaults allow agg: ibd Class

Code
  tax_agg(ps = fixed, rank = r)
Output
  psExtra object - a phyloseq object with extra slots:

  phyloseq-class experiment-level object
  otu_table()   OTU Table:         [ 19 taxa and 91 samples ]
  sample_data() Sample Data:       [ 91 samples by 15 sample variables ]
  tax_table()   Taxonomy Table:    [ 19 taxa by 3 taxonomic ranks ]

  psExtra info:
  tax_agg = "Class"

tax_fix defaults allow agg: ibd Order

Code
  tax_agg(ps = fixed, rank = r)
Output
  psExtra object - a phyloseq object with extra slots:

  phyloseq-class experiment-level object
  otu_table()   OTU Table:         [ 32 taxa and 91 samples ]
  sample_data() Sample Data:       [ 91 samples by 15 sample variables ]
  tax_table()   Taxonomy Table:    [ 32 taxa by 4 taxonomic ranks ]

  psExtra info:
  tax_agg = "Order"

tax_fix defaults allow agg: ibd Family

Code
  tax_agg(ps = fixed, rank = r)
Output
  psExtra object - a phyloseq object with extra slots:

  phyloseq-class experiment-level object
  otu_table()   OTU Table:         [ 59 taxa and 91 samples ]
  sample_data() Sample Data:       [ 91 samples by 15 sample variables ]
  tax_table()   Taxonomy Table:    [ 59 taxa by 5 taxonomic ranks ]

  psExtra info:
  tax_agg = "Family"

tax_fix defaults allow agg: ibd Genus

Code
  tax_agg(ps = fixed, rank = r)
Output
  psExtra object - a phyloseq object with extra slots:

  phyloseq-class experiment-level object
  otu_table()   OTU Table:         [ 178 taxa and 91 samples ]
  sample_data() Sample Data:       [ 91 samples by 15 sample variables ]
  tax_table()   Taxonomy Table:    [ 178 taxa by 6 taxonomic ranks ]

  psExtra info:
  tax_agg = "Genus"

tax_fix defaults allow agg: ibd Species

Code
  tax_agg(ps = fixed, rank = r)
Output
  psExtra object - a phyloseq object with extra slots:

  phyloseq-class experiment-level object
  otu_table()   OTU Table:         [ 178 taxa and 91 samples ]
  sample_data() Sample Data:       [ 91 samples by 15 sample variables ]
  tax_table()   Taxonomy Table:    [ 178 taxa by 7 taxonomic ranks ]

  psExtra info:
  tax_agg = "Species"

david-barnett/microViz documentation built on April 17, 2025, 4:25 a.m.