For a prep Recipe adds a consensus strategies to use for result extraction.
Usage
bake(
rec,
count_cutoff = NULL,
weights = NULL,
exclude = NULL,
id = rand_id("bake")
)
# S4 method for class 'PrepRecipe'
bake(
rec,
count_cutoff = NULL,
weights = NULL,
exclude = NULL,
id = rand_id("bake")
)
# S4 method for class 'Recipe'
bake(
rec,
count_cutoff = NULL,
weights = NULL,
exclude = NULL,
id = rand_id("bake")
)Arguments
- rec
A Recipe object. The step will be added to the sequence of operations for this Recipe.
- count_cutoff
Indicates the minimum number of methods in which an OTU must be present (Default: NULL). If count_cutoff is NULL count_cutoff is equal to
length(steps_ids(rec, "da")) - length(exclude)- weights
Named vector with the ponderation value for each method.
- exclude
Method ids to exclude.
- id
A character string that is unique to this step to identify it.
Examples
data(test_prep_rec)
rec <- test_prep_rec
## Default bake extracts common OTUs in all DA tested methods
## (In this case the Recipe contains 3 methods)
res <- bake(rec)
cool(res)
#> ℹ Bake for count_cutoff = 3
#> # A tibble: 23 × 2
#> taxa_id taxa
#> <chr> <chr>
#> 1 Otu_96 Prevotella
#> 2 Otu_340 Holdemanella
#> 3 Otu_332 Catenibacterium
#> 4 Otu_119 Alistipes
#> 5 Otu_45 Slackia
#> 6 Otu_82 Barnesiella
#> 7 Otu_78 Bacteroides
#> 8 Otu_88 Odoribacter
#> 9 Otu_259 Coprococcus
#> 10 Otu_35 Collinsella
#> # ℹ 13 more rows
## bake and cool methods needs a PrepRecipe. If you pass a non-PrepRecipe
## the output is an error.
data(test_rec)
err <- testthat::expect_error(bake(test_rec))
err
#> <error/rlang_error>
#> Error in `bake()`:
#> ! This function needs a PrepRecipe!
#> • Run prep(rec) and then try with bake()
#> ---
#> Backtrace:
#> ▆
#> 1. └─pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
#> 2. └─pkgdown::build_site(...)
#> 3. └─pkgdown:::build_site_local(...)
#> 4. └─pkgdown::build_reference(...)
#> 5. ├─pkgdown:::unwrap_purrr_error(...)
#> 6. │ └─base::withCallingHandlers(...)
#> 7. └─purrr::map(...)
#> 8. └─purrr:::map_("list", .x, .f, ..., .progress = .progress)
#> 9. ├─purrr:::with_indexed_errors(...)
#> 10. │ └─base::withCallingHandlers(...)
#> 11. ├─purrr:::call_with_cleanup(...)
#> 12. └─pkgdown (local) .f(.x[[i]], ...)
#> 13. ├─base::withCallingHandlers(...)
#> 14. └─pkgdown:::data_reference_topic(...)
#> 15. └─pkgdown:::run_examples(...)
#> 16. └─pkgdown:::highlight_examples(code, topic, env = env)
#> 17. └─downlit::evaluate_and_highlight(...)
#> 18. └─evaluate::evaluate(code, child_env(env), new_device = TRUE, output_handler = output_handler)
#> 19. └─evaluate:::evaluate_call(...)
#> 20. ├─evaluate (local) timing_fn(...)
#> 21. ├─evaluate (local) handle(...)
#> 22. │ └─base::try(f, silent = TRUE)
#> 23. │ └─base::tryCatch(...)
#> 24. │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
#> 25. │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
#> 26. │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
#> 27. ├─base::withCallingHandlers(...)
#> 28. ├─base::withVisible(...)
#> 29. └─evaluate:::eval_with_user_handlers(expr, envir, enclos, user_handlers)
#> 30. └─base::eval(expr, envir, enclos)
#> 31. └─base::eval(expr, envir, enclos)
#> 32. ├─testthat::expect_error(bake(test_rec))
#> 33. │ └─testthat:::expect_condition_matching(...)
#> 34. │ └─testthat:::quasi_capture(...)
#> 35. │ ├─testthat (local) .capture(...)
#> 36. │ │ └─base::withCallingHandlers(...)
#> 37. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
#> 38. ├─dar::bake(test_rec)
#> 39. └─dar::bake(test_rec)
## We can use the parameter `cout_cutoff` to for example select those OTUs
## shared with at least two methods
res <- bake(rec, count_cutoff = 2)
cool(res)
#> ℹ Bake for count_cutoff = 2
#> # A tibble: 34 × 2
#> taxa_id taxa
#> <chr> <chr>
#> 1 Otu_96 Prevotella
#> 2 Otu_340 Holdemanella
#> 3 Otu_332 Catenibacterium
#> 4 Otu_119 Alistipes
#> 5 Otu_45 Slackia
#> 6 Otu_82 Barnesiella
#> 7 Otu_78 Bacteroides
#> 8 Otu_88 Odoribacter
#> 9 Otu_259 Coprococcus
#> 10 Otu_35 Collinsella
#> # ℹ 24 more rows
## Furthermore, we can exclude methods from the consensus strategy with the
## `exclude` parameter.
res <- bake(rec, exclude = steps_ids(rec, "da")[1])
cool(res)
#> ℹ Bake for count_cutoff = 2
#> ℹ Results from maaslin__ChaSan are excluded
#> # A tibble: 34 × 2
#> taxa_id taxa
#> <chr> <chr>
#> 1 Otu_371 Megasphaera
#> 2 Otu_361 Phascolarctobacterium
#> 3 Otu_392 Parasutterella
#> 4 Otu_214 Clostridium
#> 5 Otu_365 Mitsuokella
#> 6 Otu_332 Catenibacterium
#> 7 Otu_34 Olsenella
#> 8 Otu_119 Alistipes
#> 9 Otu_397 Bilophila
#> 10 Otu_407 Anaerobiospirillum
#> # ℹ 24 more rows
## Finally, we can use the `weights` parameter to weigh each method.
weights <- c(2, 1, 1)
names(weights) <- steps_ids(rec, "da")
res <- bake(rec, weights = weights)
cool(res)
#> ℹ Bake for count_cutoff = 3
#> # A tibble: 34 × 2
#> taxa_id taxa
#> <chr> <chr>
#> 1 Otu_96 Prevotella
#> 2 Otu_340 Holdemanella
#> 3 Otu_332 Catenibacterium
#> 4 Otu_119 Alistipes
#> 5 Otu_45 Slackia
#> 6 Otu_82 Barnesiella
#> 7 Otu_78 Bacteroides
#> 8 Otu_88 Odoribacter
#> 9 Otu_259 Coprococcus
#> 10 Otu_35 Collinsella
#> # ℹ 24 more rows