Species Summary

Returns an enriched per-species summary as a tibble. Provides more detail than species(), which returns only a character vector.

Usage

speciesSummary(object, ...)

# S4 method for class 'ConsortiumMetabolism'
speciesSummary(object, ...)

# S4 method for class 'ConsortiumMetabolismAlignment'
speciesSummary(object, ...)

# S4 method for class 'ConsortiumMetabolismSet'
speciesSummary(object, ...)

Arguments

object

A ConsortiumMetabolismSet object.

...

Additional arguments passed to methods.

Value

A tibble with per-species metrics. Columns depend on the class:

• ConsortiumMetabolism: species, n_pathways, n_consumed, n_produced.

• ConsortiumMetabolismSet: species, n_consortia, n_pathways.

• ConsortiumMetabolismAlignment (pairwise): species, role ("shared", "unique_query", or "unique_reference").

Methods (by class)

• speciesSummary(ConsortiumMetabolism): Species summary for a ConsortiumMetabolism

• speciesSummary(ConsortiumMetabolismAlignment): Species summary for a ConsortiumMetabolismAlignment. Only available for pairwise alignments.

• speciesSummary(ConsortiumMetabolismSet): Species summary for a ConsortiumMetabolismSet

Examples

cm <- synCM("test", n_species = 3, max_met = 5)
speciesSummary(cm)
#> # A tibble: 3 × 4
#>   species  n_pathways n_consumed n_produced
#>   <chr>         <int>      <int>      <int>
#> 1 VVG1917O          6          2          3
#> 2 SPU7917S          2          1          2
#> 3 YLH6037K          1          1          1