plot_tox_endpoints2: EndPoint boxplots with faceting option

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

EndPoint boxplots with faceting option

Description

The plot_tox_endpoints2 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".

Usage

plot_tox_endpoints2(
  cs,
  ...,
  category = "Chemical",
  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

cs	Data.frame from get_chemical_summary.
...	Additional group_by arguments. This can be handy for creating facet graphs.
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

The difference between this function and the plot_tox_endpoints is that the ... arguments allow for customized faceting. To include this in the original toxEval function, backward compatibility would be broken.

Examples

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)
cs <- get_chemical_summary(tox_list, ACC, filtered_ep)
cs$guide_side <- "A"

cs2 <- cs
cs2$guide_side <- "B"

cs_double <- rbind(cs, cs2)

plot_tox_endpoints2(cs_double, guide_side,
  top_num = 10
) +
  ggplot2::facet_grid(. ~ guide_side, scales = "free_x")

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