Compare Two Species by Pathway Set

Computes similarity metrics between the pathway sets of two species. Two dispatch modes are supported:

• compareSpecies(cm, sp1, sp2): compare two species within the same ConsortiumMetabolism object.

• compareSpecies(cm1, cm2, sp1, sp2): compare one species from each of two ConsortiumMetabolism objects (e.g. the same species under different growth conditions).

The pathway set for a species is the set of (consumed, produced) pairs in which that species participates.

Usage

compareSpecies(x, y, ...)

# S4 method for class 'ConsortiumMetabolism,character'
compareSpecies(x, y, sp2, ...)

# S4 method for class 'ConsortiumMetabolism,ConsortiumMetabolism'
compareSpecies(x, y, sp1, sp2, ...)

Arguments

x

A ConsortiumMetabolism object (first).

y

A ConsortiumMetabolism object (second).

...

For same-CM: sp2 (character scalar naming the second species). For cross-CM: sp1 and sp2 (character scalars naming one species from each consortium).

sp2

Character scalar; species from y.

sp1

Character scalar; species from x.

Value

A named list with elements:

fos

Szymkiewicz-Simpson overlap score (intersection over min set size).

jaccard

Jaccard similarity (intersection over union).

n_shared

Number of shared pathways.

n_unique_sp1

Pathways only in sp1.

n_unique_sp2

Pathways only in sp2.

Methods (by class)

• compareSpecies(x = ConsortiumMetabolism, y = character): Compare two species within the same ConsortiumMetabolism

• compareSpecies(x = ConsortiumMetabolism, y = ConsortiumMetabolism): Compare one species from each of two ConsortiumMetabolism objects

Examples

cm <- synCM("test", n_species = 3, max_met = 5)
sp <- species(cm)
compareSpecies(cm, sp[1], sp[2])
#> $fos
#> [1] 0.3333333
#> 
#> $jaccard
#> [1] 0.125
#> 
#> $n_shared
#> [1] 1
#> 
#> $n_unique_sp1
#> [1] 2
#> 
#> $n_unique_sp2
#> [1] 5
#>