plot_tox_endpoints: EndPoint boxplots

In USGS-R/toxEval: Exploring Biological Relevance of Environmental Chemistry Observations

EndPoint boxplots

Description

The plot_tox_endpoints function creates a set of boxplots representing EAR values for each endPoint based on the selected data. A subset of data is first chosen by specifying a group in the filterBy argument. The filterBy argument must match one of the unique options in the category. For example, if the category is "Chemical Class", then the filterBy argument must be one of the defined "Chemical Class" options such as "Herbicide". A boxplot is generated for each endPoint. The EAR values that are used to create the boxplots are the mean or maximum (as defined by mean_logic) for each site as described in "Summarizing the data"in the Introduction vignette: vignette("Introduction", package = "toxEval").

Usage

plot_tox_endpoints(
  chemical_summary,
  category = "Biological",
  filterBy = "All",
  manual_remove = NULL,
  hit_threshold = NA,
  mean_logic = FALSE,
  sum_logic = TRUE,
  font_size = NA,
  title = NA,
  x_label = NA,
  palette = NA,
  top_num = NA
)

Arguments

chemical_summary	Data frame from get_chemical_summary.
category	Either "Biological", "Chemical Class", or "Chemical".
filterBy	Character. Either "All" or one of the filtered categories.
manual_remove	Vector of categories to remove.
hit_threshold	Numeric threshold defining a "hit".
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.
font_size	Numeric to adjust the axis font size.
title	Character title for plot.
x_label	Character for x label. Default is NA which produces an automatic label.
palette	Vector of color palette for fill. Can be a named vector to specify specific color for specific categories.
top_num	Integer number of endpoints to include in the graph. If NA, all endpoints will be included.

Details

Box plots are standard Tukey representations. See "Box plot details" in the Basic Workflow vignette: vignette("basicWorkflow", package = "toxEval") for more information.

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_endpoints(chemical_summary,
  filterBy = "Cell Cycle",
  top_num = 10
)

plot_tox_endpoints(chemical_summary,
  filterBy = "Cell Cycle",
  top_num = 10,
  x_label = "EAR"
)

plot_tox_endpoints(chemical_summary,
  category = "Chemical Class", filterBy = "PAHs",
  top_num = 10, hit_threshold = 0.001
)

plot_tox_endpoints(chemical_summary, category = "Chemical", filterBy = "Atrazine")
plot_tox_endpoints(chemical_summary, category = "Chemical", top_num = 10)
single_site <- dplyr::filter(chemical_summary, site == "USGS-04024000")
plot_tox_endpoints(single_site, category = "Chemical", top_num = 10)

USGS-R/toxEval documentation built on Feb. 9, 2024, 6:24 p.m.