tests/testthat/_snaps/tax_agg.md

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

microbiome's dietswap data hasn't changed

Code
  dietswap
Output
  phyloseq-class experiment-level object
  otu_table()   OTU Table:         [ 130 taxa and 222 samples ]
  sample_data() Sample Data:       [ 222 samples by 8 sample variables ]
  tax_table()   Taxonomy Table:    [ 130 taxa by 3 taxonomic ranks ]

tax_agg gives appropriate errors

psExtra object - a phyloseq object with extra slots:

phyloseq-class experiment-level object
otu_table()   OTU Table:         [ 130 taxa and 222 samples ]
sample_data() Sample Data:       [ 222 samples by 8 sample variables ]
tax_table()   Taxonomy Table:    [ 130 taxa by 4 taxonomic ranks ]

psExtra info:
tax_agg = "unique"

microbiome::aggregate_taxa output hasn't changed: Phylum

Code
  microbiome::aggregate_taxa(x = dietswap, level = level)
Output
  phyloseq-class experiment-level object
  otu_table()   OTU Table:         [ 8 taxa and 222 samples ]
  sample_data() Sample Data:       [ 222 samples by 8 sample variables ]
  tax_table()   Taxonomy Table:    [ 8 taxa by 2 taxonomic ranks ]

microViz::tax_agg output hasn't changed: Phylum

Code
  ps_get(tax_agg(ps = dietswap, level, sort_by = "name", add_unique = TRUE))
Output
  phyloseq-class experiment-level object
  otu_table()   OTU Table:         [ 8 taxa and 222 samples ]
  sample_data() Sample Data:       [ 222 samples by 8 sample variables ]
  tax_table()   Taxonomy Table:    [ 8 taxa by 2 taxonomic ranks ]

microbiome::aggregate_taxa output hasn't changed: Family

Code
  microbiome::aggregate_taxa(x = dietswap, level = level)
Output
  phyloseq-class experiment-level object
  otu_table()   OTU Table:         [ 22 taxa and 222 samples ]
  sample_data() Sample Data:       [ 222 samples by 8 sample variables ]
  tax_table()   Taxonomy Table:    [ 22 taxa by 3 taxonomic ranks ]

microViz::tax_agg output hasn't changed: Family

Code
  ps_get(tax_agg(ps = dietswap, level, sort_by = "name", add_unique = TRUE))
Output
  phyloseq-class experiment-level object
  otu_table()   OTU Table:         [ 22 taxa and 222 samples ]
  sample_data() Sample Data:       [ 222 samples by 8 sample variables ]
  tax_table()   Taxonomy Table:    [ 22 taxa by 3 taxonomic ranks ]

tax_fix error prompt looks right

Code
  cat(taxFixPrompt())
Output


  To fix the problem, try:
    `yourData %>% tax_fix()`

  Try tax_fix_interactive() to find and fix further problems

Code
  cat(taxFixPrompt(unknowns = c("anUnknown", "another")))
Output


  To fix the problem, try:
    `yourData %>% tax_fix(unknowns = c("anUnknown", "another"))`

  Try tax_fix_interactive() to find and fix further problems

tax_agg errors on NAs, '', or convergent values

Code
  tax_agg(dietswap, rank = "Genus")
Condition
  Error in `tax_agg()`:
  ! NAs in tax_table at rank: Genus

  To fix the problem, try:
    `yourData %>% tax_fix()`

  Try tax_fix_interactive() to find and fix further problems

Code
  tax_agg(dietswap, rank = "Genus")
Condition
  Error in `tax_agg()`:
  ! zero-length name(s) in tax_table at rank: Genus

  To fix the problem, try:
    `yourData %>% tax_fix()`

  Try tax_fix_interactive() to find and fix further problems

Code
  tax_agg(dietswap, rank = "Genus")
Message
  Problematic Genus values detected in tax_table:
  g__

  Convergent rows:
    `Taxon name`                      Phylum          Family                 Genus
  1 Aeromonas                         Proteobacteria  Proteobacteria         g__  
  2 Akkermansia                       Verrucomicrobia Verrucomicrobia        g__  
  3 Allistipes et rel.                Bacteroidetes   Bacteroidetes          g__  
  4 Anaerofustis                      Firmicutes      Clostridium cluster XV g__  
  5 Anaerostipes caccae et rel.       Firmicutes      Clostridium cluster X~ g__  
  6 Anaerotruncus colihominis et rel. Firmicutes      Clostridium cluster IV g__  
Condition
  Error:
  ! Taxa cannot be aggregated at rank: Genus
  See last message for convergent taxa rows.

  To fix the problem, try:
    `yourData %>% tax_fix(unknowns = c("g__"))`

  Try tax_fix_interactive() to find and fix further problems

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