toxEval (version 1.4.0)

plot_tox_stacks: Plot stacked bar charts

Description

The plot_tox_stacks function creates a set of boxplots representing EAR values computed with the get_chemical_summary function, and dependent on the choice of several input options. See "Summarizing the data" in the Introduction vignette: vignette("Introduction", package = "toxEval") for a description on how the EAR values are computed, aggregated, and summarized. Choosing "Chemical Class" in the category argument will generate separate stacked bars for each unique class. "Chemical" will generate stacked bars for each individual chemical, and "Biological" will generate stacked bars for each group in the selected ToxCast annotation. The legend can optionally be turned on or off using the include_legend argument. It may be impractical for instance to show the legend for "Chemical" if there are hundreds of chemicals.

Usage

plot_tox_stacks(
  chemical_summary,
  chem_site,
  category = "Biological",
  mean_logic = FALSE,
  sum_logic = TRUE,
  manual_remove = NULL,
  include_legend = TRUE,
  font_size = NA,
  title = NA,
  y_label = NA,
  top_num = NA
)

Arguments

chemical_summary

Data frame from get_chemical_summary.

chem_site

Data frame with at least columns SiteID, site_grouping, and Short Name.

category

Character. Either "Biological", "Chemical Class", or "Chemical".

mean_logic

Logical. TRUE displays the mean sample from each site, FALSE displays the maximum sample from each site.

sum_logic

Logical. TRUE sums the EARs in a specified grouping, FALSE does not. FALSE may be better for traditional benchmarks as opposed to ToxCast benchmarks.

manual_remove

Vector of categories to remove.

include_legend

Logical. Used to include legend or not.

font_size

Numeric value to adjust the axis font size.

title

Character title for plot.

y_label

Character for x label. Default is NA which produces an automatic label.

top_num

Integer number to include in the graph. If NA, all data will be included.

Details

The graph displays a slightly different result for a single site. Providing data with only one site displays each individual sample as a stacked bar rather than the mean or maximum for a site.

This is a function where it may be ideal to create a custom order to the sites (for example, west-to-east). See the above section "Custom configuration" vignette("Introduction", package = "toxEval") for instructions on how to convert the character vector sites to a factor with ordered levels.

Examples

# This is the example workflow:
path_to_tox <- system.file("extdata", package = "toxEval")
file_name <- "OWC_data_fromSup.xlsx"

full_path <- file.path(path_to_tox, file_name)

tox_list <- create_toxEval(full_path)

ACC <- get_ACC(tox_list$chem_info$CAS)
ACC <- remove_flags(ACC)

cleaned_ep <- clean_endPoint_info(end_point_info)
filtered_ep <- filter_groups(cleaned_ep)
chemical_summary <- get_chemical_summary(tox_list, ACC, filtered_ep)

plot_tox_stacks(chemical_summary, tox_list$chem_site, 
                "Biological", top_num = 5)

# \donttest{
plot_tox_stacks(chemical_summary, tox_list$chem_site, "Chemical Class")
plot_tox_stacks(chemical_summary, tox_list$chem_site, "Chemical", include_legend = FALSE)
plot_tox_stacks(chemical_summary, tox_list$chem_site, "Chemical", top_num = 5, y_label = "EAR")

single_site <- dplyr::filter(chemical_summary, site == "USGS-04024000")
plot_tox_stacks(single_site, tox_list$chem_site, "Chemical", top_num = 5)
plot_tox_stacks(single_site,
  chem_site = tox_list$chem_site,
  category = "Chemical", top_num = 5, y_label = "EAR"
)
# }