Using the Shiny Application

The Shiny application (the app) is a quick and convenient way to explore data through a graphical user interface in the user’s default browser. As with the R-package, ToxCast is the default biological endpoint database used to evaluate data. A user can override this default by providing a custom set of endpoints (e.g. aquatic life benchmarks).

The interaction with the app is primarily “point and click”. The app includes multiple ways to visualize data through boxplots, barcharts, tables and an overview map. Numerous options can be selected to customize presentation of data by choosing to focus on chemicals, chemical classes, biologically relevant endpoing groupings, and specific suites of ToxCast assays. All resulting graphics, tables, and data can be downloaded for use outside of the app.

While the app is useful and quite flexible as is, it also serves as a good starting point for a more in-depth user- and study-specific analysis. All of the output on the Shiny app can be created directly in R as well. For flexibility beyond what the app offers, the R-code to produce each graph and table is displayed in the app. The user may copy this code into a script and customize it for specific study needs. The help file for each function provides instructions and example workflows (R code) for their use.

To run the app, load the toxEval package, and run the explore_endpoints function:

The computer’s default browser will open up and display the following page:

The app can be divided into 3 main sections:

The left sidebar (with the black background) is used to load the data and set up the conditions for analysis. Options for this section are described in the “Sidebar” section below.

The main visualization display section includes a variety of tabs to choose from to explore the data in different ways. Each section is described in the section “Main Output”.

The bottom section, “R Code:”, displays the R code to reproduce the analysis directly in R using the toxEval R-package functions. The code can be copied and pasted directly into the R console, or (preferred for reproduciblity!) saved in an R script. Information on this option is provided below in the “R Code” section.

Main Output

Each plot and table offered in the app is described in the Basic Workflow vignette. Please refer there for more information.

Each plot, table, and the map are generated by functions within the R-package. The table to the right indicates the function used for each tab in the app.

All resulting graphics, tables, and data can be downloaded for use outside of the app. Graphics are downloaded in “png” format and tables and data are are downloaded in “csv” format. In addition, R code to reproduce each analysis in the R environment is provided at the bottom of each tab. See the “R Code” section for details.

Tab Function
Map make_tox_map
Box Plots plot_tox_boxplots
Bar Charts plot_tox_stacks
Max EAR and Frequency rank_sites_DT
Hit Counts hits_summary_DT
Site Hits hits_by_groupings_DT
Endpoint Hits endpoint_hits_DT
Endpoint plot_tox_endpoints
Heat Map plot_tox_heatmap

R Code

Each tab is generated based on specific functions within the R-Package, and the appropriate code to reproduce results from each tab is provided at the bottom of the tab. Modification of this code in the R environment allows the user to customize plots and tables based on specific study needs.

The app provides many graphics and tables to work through a data analysis, some users may wish to have a record of what has been done, or to save specific analyses that prove to be particularly useful. By copying and pasting the R code, users by developing a “workflow” script that has all analysis saved in one place rather than needing to go through the process of choosing the many options needed to reproduce exactly what was done previously in the app. This workflow can serve as a valuable resource that results in reliably reproducible research. In the event of a need to modify a data set, it can also be used to efficiently update a data analysis without having to reproduce each step in the app manually.

Logistics

Reporting bugs

Please consider reporting bugs and asking questions on the Issues page: https://github.com/USGS-R/toxEval/issues

Citing toxEval

citation(package = "toxEval")
## 
## To cite toxEval in publications, please use:
## 
##   De Cicco, L.A., Corsi, S.R., Villeneuve D.L,
##   Blackwell, and B.R, Ankley, G.T., 2018, toxEval:
##   Evaluation of measured concentration data using the
##   ToxCast high-throughput screening database or a
##   user-defined set of concentration benchmarks. R
##   package version 1.1.0.,
##   https://code.usgs.gov/water/toxEval,
##   doi:10.5066/P906UQ5I
## 
## A BibTeX entry for LaTeX users is
## 
##   @Manual{,
##     author = {Laura A. {De Cicco} and Steven R. Corsi and Daniel L. Villeneuve and Brett R. Blackwell and Gerald T. Ankley},
##     title = {toxEval: Evaluation of measured concentration data using the ToxCast high-throughput screening database or a user-defined set of concentration benchmarks.},
##     publisher = {U.S. Geological Survey},
##     version = {1.1.0},
##     address = {Reston, VA},
##     institution = {U.S. Geological Survey},
##     year = {2019},
##     doi = {10.5066/P906UQ5I},
##     url = {https://code.usgs.gov/water/toxEval},
##   }

Disclaimer

This software has been approved for release by the U.S. Geological Survey (USGS). Although the software has been subjected to rigorous review, the USGS reserves the right to update the software as needed pursuant to further analysis and review. No warranty, expressed or implied, is made by the USGS or the U.S. Government as to the functionality of the software and related material nor shall the fact of release constitute any such warranty. Furthermore, the software is released on condition that neither the USGS nor the U.S. Government shall be held liable for any damages resulting from its authorized or unauthorized use.

Any use of trade, firm, or product names is for descriptive purposes only and does not imply endorsement by the U.S. Government.