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Histograms, density or beeswarm plots of individual metabolite values before and after imputation

create_distribution_plot.Rd

create_distribution_plot() creates density plots of metabolite values before and after imputation (with the sample limit of detection), beeswarm plots or histograms of the values before and after imputation. Histogram can also show only imputed values.

Usage

create_distribution_plot(
  dat,
  metabolite,
  type = "histogram",
  bins = 30,
  histogram_type = "all"
)

Arguments

dat

a raw_data object, the output of the read_data() function. The data have to be completed, for example using the complete_data() function.

metabolite

a name of the metabolite of interest.

type

a type of the plot. Can be either "histogram" (default), "density", "beeswarm_interactive" or "beeswarm".

bins

the number of bins for the histogram plot; 30 if not specified.

histogram_type

if "all' (default), the histogram displays all values after imputation. If "imputed", it shows only the values that were imputed.

Examples

path <- get_example_data("small_biocrates_example.xls")
dat <- read_data(path)
dat <- complete_data(dat, "limit", "limit", "limit")
#> Completing 109 < LOD values...
#> Completing 6 < LLOQ values...
#> Completing 9 < ULOQ values...
print(create_distribution_plot(dat, "C3"))
#> Warning: There was 1 warning in `mutate()`.
#> ℹ In argument: `across(all_of(metabolite), ~as.numeric(.))`.
#> Caused by warning:
#> ! NAs introduced by coercion
#> Warning: Removed 1 row containing non-finite outside the scale range (`stat_bin()`).
#> Warning: Removed 4 rows containing non-finite outside the scale range (`stat_bin()`).

print(create_distribution_plot(dat, "C3", type = "density"))
#> Warning: There was 1 warning in `mutate()`.
#> ℹ In argument: `across(all_of(metabolite), ~as.numeric(.))`.
#> Caused by warning:
#> ! NAs introduced by coercion
#> Warning: Removed 1 row containing non-finite outside the scale range (`stat_density()`).
#> Warning: Removed 4 rows containing non-finite outside the scale range
#> (`stat_density()`).

print(create_distribution_plot(dat, "C3", type = "beeswarm_interactive"))
#> Warning: There was 1 warning in `mutate()`.
#> ℹ In argument: `across(all_of(metabolite), ~as.numeric(.))`.
#> Caused by warning:
#> ! NAs introduced by coercion
#> Warning: Removed 5 rows containing missing values or values outside the scale range
#> (`position_quasirandom()`).