graph_data_prep: Prepare boxplot data

In toxEval: Exploring Biological Relevance of Environmental Chemistry Observations

Prepare boxplot data

Description

A set of functions to prepare the data for boxplots. Often, these functions are used within the plotting functions. They are exported however to allow custom graphs to be created.

Usage

graph_chem_data(
  chemical_summary,
  ...,
  manual_remove = NULL,
  mean_logic = FALSE,
  sum_logic = TRUE
)

tox_boxplot_data(
  chemical_summary,
  category = "Biological",
  manual_remove = NULL,
  mean_logic = FALSE,
  sum_logic = TRUE
)

side_by_side_data(
  gd_left,
  gd_right,
  left_title = "Left",
  right_title = "Right"
)

Arguments

chemical_summary	Data frame from get_chemical_summary.
...	Additional group_by arguments. This can be handy for creating facet graphs.
manual_remove	Vector of categories to remove.
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.
category	Character. Either "Biological", "Chemical Class", or "Chemical".
gd_left	Data frame that must include the columns chnm, Class, and either EAR or meanEAR.
gd_right	Data frame that must include the columns chnm, Class, and either EAR or meanEAR.
left_title	Character that will be associated with the "gd_left" data frame in a column named "guide_side".
right_title	Character that will be associated with the "gd_right" data frame in a column named "guide_side".

Details

The function side_by_side_data will combine two data frames, either the output of get_chemical_summary or graph_chem_data, into a single data frame. The important work here is that the chemicals and classes factor levels are ordered primarily based on "gd_left", but include "gd_right" when the contents are mismatched.

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)

chemical_summary <- get_chemical_summary(tox_list, ACC, filtered_ep)
# Let's say we want to compare 2 chemical summaries
# We'll look at one summing EARs, and with concentrations
# First, we need a chemical summary for concentrations:
chemical_summary_conc <- get_concentration_summary(tox_list)

gd_tox <- graph_chem_data(chemical_summary)
gd_conc <- graph_chem_data(chemical_summary_conc)

ch_combo <- side_by_side_data(gd_tox, gd_conc,
  left_title = "ToxCast",
  right_title = "Concentrations"
)
plot_chemical_boxplots(ch_combo, guide_side,
  x_label = ""
) +
  ggplot2::facet_grid(. ~ guide_side, scales = "free_x")

toxEval documentation built on April 15, 2023, 1:13 a.m.