Returns pathway prevalence across consortia from a multiple alignment.
Arguments
- object
A ConsortiumMetabolismAlignment object of type
"multiple".
Methods (by class)
prevalence(ConsortiumMetabolismAlignment): Pathway prevalence from a multiple ConsortiumMetabolismAlignment
Examples
# \donttest{
cm1 <- synCM("comm_1", n_species = 3, max_met = 5)
cm2 <- synCM("comm_2", n_species = 4, max_met = 6)
cms <- ConsortiumMetabolismSet(cm1, cm2, name = "test")
#>
#> ── Creating CMS "test" ─────────────────────────────────────────────────────────
#> ℹ Validating 2 <ConsortiumMetabolism> objects
#> ✔ Validating 2 <ConsortiumMetabolism> objects [14ms]
#>
#> ℹ Collecting metabolites from 2 consortia
#> ✔ Collecting metabolites from 2 consortia [31ms]
#>
#> ℹ Re-indexing 6 unique metabolites
#> ✔ Re-indexing 6 unique metabolites [27ms]
#>
#> ℹ Expanding 2 binary matrices to 6-dimensional space
#> ✔ Expanding 2 binary matrices to 6-dimensional space [24ms]
#>
#> ℹ Computing 6 x 6 levels matrix
#> ✔ Computing 6 x 6 levels matrix [25ms]
#>
#> ℹ Computing pairwise overlap (1 pairs via crossprod)
#> ✔ Computing pairwise overlap (1 pairs via crossprod) [24ms]
#>
#> ℹ Assembling pathway data from 2 consortia
#> ✔ Assembling pathway data from 2 consortia [32ms]
#>
#> ℹ Building dendrogram from 2 x 2 dissimilarity matrix
#> ✔ Building dendrogram from 2 x 2 dissimilarity matrix [23ms]
#>
#> ℹ Extracting dendrogram node positions
#> ✔ Extracting dendrogram node positions [24ms]
#>
#> ℹ Collecting 2 consortium graphs
#> ✔ CMS "test" created: 2 consortia, 6 metabolites (0.2s)
#> ℹ Collecting 2 consortium graphs
#> ✔ Collecting 2 consortium graphs [81ms]
#>
cma <- align(cms)
#> Computing multiple alignment for 2 consortia using "FOS".
prevalence(cma)
#> consumed produced nConsortia proportion
#> 1 met4 met1 1 0.5
#> 2 met5 met1 1 0.5
#> 3 met6 met1 1 0.5
#> 4 met1 met2 1 0.5
#> 5 met3 met2 1 0.5
#> 6 met4 met2 2 1.0
#> 7 met5 met2 1 0.5
#> 8 met6 met2 1 0.5
#> 9 met1 met3 1 0.5
#> 10 met2 met3 1 0.5
#> 11 met5 met3 1 0.5
#> 12 met1 met4 1 0.5
#> 13 met2 met4 1 0.5
#> 14 met1 met5 2 1.0
#> 15 met2 met5 2 1.0
#> 16 met3 met5 1 0.5
#> 17 met4 met5 1 0.5
#> 18 met2 met6 1 0.5
#> 19 met3 met6 1 0.5
#> 20 met4 met6 1 0.5
# }