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. ├─testthat::expect_error(abundance_plt(test_rec))
#>  2. │ └─testthat:::expect_condition_matching(...)
#>  3. │   └─testthat:::quasi_capture(...)
#>  4. │     ├─testthat (local) .capture(...)
#>  5. │     │ └─base::withCallingHandlers(...)
#>  6. │     └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
#>  7. ├─dar::abundance_plt(test_rec)
#>  8. └─dar::abundance_plt(test_rec)