tests/testthat/_snaps/phyloseq_validate.md

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

phyloseq_validate warns about removing all zero taxa

Some taxa_sums were zero, removing the following taxa:
    Aerococcus 
    Aneurinibacillus 
    Asteroleplasma et rel. 
    Clostridium felsineum et rel. 
    Clostridium thermocellum et rel. 
    Methylobacterium 
    Micrococcaceae
This may be caused by using `subset_samples()`.
Try using `ps_filter()` instead, with .keep_all_taxa = FALSE.
Otherwise, to avoid this warning, try filtering out taxa summing to zero with `tax_filter()`.
If you have already transformed and/or scaled your taxa, e.g. with a log transformation or scale,
seeing this warning is possible, but very unlikely and possibly a bug. Please report this.

phyloseq_validate fixes missing sam_data with message

Code
  phyloseq_validate(ps = dietswap, verbose = TRUE)
Message
  Note: Replacing missing sample_data with a dataframe of only sample_names.
  Try `ps <- phyloseq_validate(ps, verbose = FALSE)` to avoid this message
Output
  phyloseq-class experiment-level object
  otu_table()   OTU Table:         [ 130 taxa and 222 samples ]
  sample_data() Sample Data:       [ 222 samples by 1 sample variables ]
  tax_table()   Taxonomy Table:    [ 130 taxa by 3 taxonomic ranks ]

phyloseq_validate fixes missing tax_table with message

Code
  phyloseq_validate(soilrep, verbose = TRUE)
Message
  Note: Replacing missing tax_table with a 1-column table of only taxa_names.
  Try `ps <- phyloseq_validate(ps, verbose = FALSE)` to avoid this message
Output
  phyloseq-class experiment-level object
  otu_table()   OTU Table:         [ 16825 taxa and 56 samples ]
  sample_data() Sample Data:       [ 56 samples by 4 sample variables ]
  tax_table()   Taxonomy Table:    [ 16825 taxa by 1 taxonomic ranks ]

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