Getting Started with teal

Introduction

teal is a shiny-based interactive exploration framework for analyzing data, with particular emphasis on CDISC clinical trial data. teal applications allow their users to:

“Pull” in data from external data sources
Dynamically filter of data to be used in the analyses
Generate reproducible code to regenerate the on-screen analyses
Create and download reports containing results of analyses (for analysis modules which support reporting)

In addition, the teal framework provides application developers with:

A large suite of custom-made standard analysis modules to be included in applications
A logging framework to facilitate debugging of applications

More advanced users of the framework can also create new analysis modules which can be added into any teal applications.

Your first `teal` application:

This simple teal application takes the iris and mtcars datasets and displays their contents:

library(teal)

app <- init(
  data = teal_data(IRIS = iris, MTCARS = mtcars),
  modules = modules(
    example_module("Module 1"),
    example_module("Module 2")
  ),
  filter = teal_slices(
    teal_slice(dataname = "IRIS", varname = "Species", selected = "setosa")
  ),
  title = build_app_title(title = "My first teal app"),
  header = h3("My first teal application"),
  footer = div(a("Powered by teal", href = "https://insightsengineering.github.io/teal/latest-tag/"))
)

if (interactive()) {
  shinyApp(app$ui, app$server)
}

Hovering the image shows the teal application generated by this code.

Example application Example application (hover)

Every teal application is composed of the following elements, all of which can be controlled by the app developer by passing arguments to the init function:

Application Title (browser’s tab title): is the title of the application.
Application Header and Footer (the top and the bottom of the app): any content to be placed at the top and bottom of the application.
Teal Modules (tabs under the header): tab for each module included in the application.
- In the example code: there are two modules named “Module 1” and “Module 2”.
Module Content (panel on the middle): the outputs of the currently active module.
Filter Panel (panel on the right hand side): for filtering the data to be passed into all teal modules.
- In the example code: the filter panel is being initialized with a filter for the Species variable in the iris dataset.

Creating your own applications

The key function to use to create your teal application is init, which requires two mandatory arguments: data and modules. There are other optional arguments for init, which can be used to customize the application. Please refer to the documentation for init for further details.

Application data

The data argument in the init function specifies the data used in your application. All datasets which are about to be used in teal application must be passed through teal_data object. It is also possible to specify relationships between the datasets using the join_keys argument but in this case the datasets are not related. See this vignette for details. If data is not available and has to be pulled from a remote source, init must receive a teal_data_module that specifies how to obtain the desired datasets and put them into a teal_data object. See this vignette for details.

In order to use CDISC clinical trial data in a teal application the cdisc_data function is used instead. Custom SDTM standards can be handled with teal_data and join_keys.

For further details, we recommend exploring the teal.data package documentation.

Modules

The modules argument to init consists of a list of teal modules (which can be wrapped together using the function modules). Core teal developers have created several universal teal modules that can be useful in any teal application. To learn how to create your own modules, please explore Creating Custom Modules vignette. To use our predefined modules, see the references below for links to these modules.

Defining filters

The optional filter argument in init allows you to initialize the application with predefined filters. For further details see Filter Panel vignette .

Reporting

If any of the modules in your teal application support reporting (see teal.reporter for more details), users of your application can add the outputs of the modules to a report. This report can then be downloaded and a special Report Previewer module will be added to your application as an additional tab, where users can view and configure their reports before downloading them. See more details in this vignette.

Reproducible code

teal hands over data with reproducible code to every module included in the application. Note that teal does not display the code, that is the modules’ responsibility. For example, the example_module function used above shows the code in the main panel together with other outputs. For more details see this vignette.

Where to go next

To learn more about the teal framework we recommend first exploring some of the available analysis modules.

For example see:

For a demo of teal apps see:

The teal framework relies on a set of supporting packages whose documentation provides more in-depth information. The packages which are of most interest when defining tealapplications are:

teal.data: defining data for teal application.
teal.slice: defining data filtering before passing into teal modules.

NEST CoreDev