Abundance boxplot

Usage

abundance_plt(
  rec,
  taxa_ids = NULL,
  type = "boxplot",
  transform = "compositional",
  scale = 1,
  top_n = 20
)

# S4 method for class 'Recipe'
abundance_plt(
  rec,
  taxa_ids = NULL,
  type = "boxplot",
  transform = "compositional",
  scale = 1,
  top_n = 20
)

# S4 method for class 'PrepRecipe'
abundance_plt(
  rec,
  taxa_ids = NULL,
  type = "boxplot",
  transform = "compositional",
  scale = 1,
  top_n = 20
)

Arguments

rec: A Recipe or Recipe step.
taxa_ids: Character vector with taxa_ids to plot. If taxa_ids is NULL the significant characteristics present in all of the executed methods will be plotted.
type: Character vector indicating the type of the result. Options: c("boxoplot", "heatmap").
transform: Transformation to apply. The options include: 'compositional' (ie relative abundance), 'Z', 'log10', 'log10p', 'hellinger', 'identity', 'clr', 'alr', or any method from the vegan::decostand function. If the value is NULL, no normalization is applied and works with the raw counts.
scale: Scaling constant for the abundance values when transform = "scale".
top_n: Maximum number of taxa to represent. Default: 20.

Value

ggplot2

Examples

data(test_prep_rec)

## Running the function returns a boxplot,
abundance_plt(test_prep_rec)
#> ! Taxa present in all methods are greater than the cutoff top_n = 20
#> ℹ The top 20 significant taxa with the greatest overlap between methods will be used


## Giving the value "heatmap" to the type parameter, the resulting graph
## a heatmap.
# abundance_plt(test_prep_rec, type = "heatmap")

## By default, those taxa significant in all methods are plotted. If you want
## to graph some determined features, you can pass them as vector through the
## taxa_ids parameter.
# taxa_ids <- c("Otu_96", "Otu_78", "Otu_88", "Otu_35", "Otu_94", "Otu_34")
# abundance_plt(test_prep_rec, taxa_ids = taxa_ids)
# abundance_plt(test_prep_rec, taxa_ids = taxa_ids, type = "heatmap")

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