Overlap of significant OTUs between tested methods.

Overlap of significant OTUs between tested methods.

Usage

overlap_df(rec, steps = steps_ids(rec, "da"), type = "all")

# S4 method for class 'Recipe'
overlap_df(rec, steps = steps_ids(rec, "da"), type = "all")

# S4 method for class 'PrepRecipe'
overlap_df(rec, steps = steps_ids(rec, "da"), type = "all")

Arguments

rec

A Recipe object.

steps

Character vector with step_ids to take in account.

type

Indicates whether to use all taxa ("all") or only those that are differentially abundant in at least one method ("da"). Default as "all".

Value

df

Examples

data(test_prep_rec)

## Running the function returns a UpSet plot ordered by frequency.
df <- overlap_df(test_prep_rec, steps_ids(test_prep_rec, "da"))
head(df)
#>                       maaslin__ChaSan metagenomeseq__Zlebia deseq__Linzer_torte
#> maaslin__ChaSan             1.0000000             0.4257426           0.4158416
#> metagenomeseq__Zlebia       0.4257426             1.0000000           0.8712871
#> deseq__Linzer_torte         0.4158416             0.8712871           1.0000000

## If you want to exclude a method for the plot, you can remove it with the
## step parameter. In the following example we eliminate from the graph the
## results of maaslin
overlap_df(test_prep_rec, steps = steps_ids(test_prep_rec, "da")[-1])
#>                       metagenomeseq__Zlebia deseq__Linzer_torte
#> metagenomeseq__Zlebia             1.0000000           0.8712871
#> deseq__Linzer_torte               0.8712871           1.0000000

## overlap_df function needs a prep-Recipe. If you pass a a non-prep
## Recipe the output is an error.
data(test_rec)
err <- testthat::expect_error(overlap_df(test_rec))
err
#> <error/rlang_error>
#> Error in `overlap_df()`:
#> ! This function needs a PrepRecipe!
#> • Run prep(rec) and then try with overlap_df()
#> ---
#> 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.                         ├─base::withRestarts(...)
#>  20.                         │ └─base (local) withRestartList(expr, restarts)
#>  21.                         │   ├─base (local) withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
#>  22.                         │   │ └─base (local) doWithOneRestart(return(expr), restart)
#>  23.                         │   └─base (local) withRestartList(expr, restarts[-nr])
#>  24.                         │     ├─base (local) withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
#>  25.                         │     │ └─base (local) doWithOneRestart(return(expr), restart)
#>  26.                         │     └─base (local) withRestartList(expr, restarts[-nr])
#>  27.                         │       └─base (local) withOneRestart(expr, restarts[[1L]])
#>  28.                         │         └─base (local) doWithOneRestart(return(expr), restart)
#>  29.                         ├─evaluate:::with_handlers(...)
#>  30.                         │ ├─base::eval(call)
#>  31.                         │ │ └─base::eval(call)
#>  32.                         │ └─base::withCallingHandlers(...)
#>  33.                         ├─base::withVisible(eval(expr, envir))
#>  34.                         └─base::eval(expr, envir)
#>  35.                           └─base::eval(expr, envir)
#>  36.                             ├─testthat::expect_error(overlap_df(test_rec))
#>  37.                             │ └─testthat:::expect_condition_matching(...)
#>  38.                             │   └─testthat:::quasi_capture(...)
#>  39.                             │     ├─testthat (local) .capture(...)
#>  40.                             │     │ └─base::withCallingHandlers(...)
#>  41.                             │     └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
#>  42.                             ├─dar::overlap_df(test_rec)
#>  43.                             └─dar::overlap_df(test_rec)