Plot otuput of the overlap_df function as a heatmap.

Plot otuput of the overlap_df function as a heatmap.

Usage

corr_heatmap(rec, steps = steps_ids(rec, "da"), font_size = 15, type = "all")

# S4 method for class 'Recipe'
corr_heatmap(rec, steps = steps_ids(rec, "da"), font_size = 15, type = "all")

# S4 method for class 'PrepRecipe'
corr_heatmap(rec, steps = steps_ids(rec, "da"), font_size = 15, type = "all")

Arguments

rec

A Recipe object.

steps

Character vector with step_ids to take in account.

font_size

Size of the axis font.

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

heatmap

Examples

data(test_prep_rec)

## Running the function returns a UpSet plot ordered by frequency.
corr_heatmap(test_prep_rec)


## 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
corr_heatmap(test_prep_rec, steps = steps_ids(test_prep_rec, "da")[-1])


## corr_heatmap function needs a PrepRecipe. If you pass a a non-prep
## Recipe the output is an error.
data(test_rec)
err <- testthat::expect_error(corr_heatmap(test_rec))
err
#> <error/rlang_error>
#> Error in `corr_heatmap()`:
#> ! This function needs a PrepRecipe!
#> • Run prep(rec) and then try with corr_heatmap()
#> ---
#> 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(corr_heatmap(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::corr_heatmap(test_rec)
#>  43.                             └─dar::corr_heatmap(test_rec)