Creating Custom Modules

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NEST CoreDev

Introduction

The teal framework provides a large catalog of plug-in-ready analysis modules to be incorporated into teal applications. However, it is also possible to create your own modules using the module function.

Components of a module

UI function

This function contains the UI required for the module. It should be a function with at least the argument id. See the server section below for more details.

Server function

This function contains the shiny server logic for the module and should be of the form:

function(
    id,
    data, # optional; use if module needs access to application data
    filter_panel_api, # optional; use if module needs access to filter panel; see teal.slice
    reporter, # optional; use if module supports reporting; see reporting vignette
    ...) {
  moduleServer(id, function(input, output, session) {
    # module code here
  })
}

The data that arrives in the module is a teal_data object, the data container used throughout the teal application. teal_data is passed to the init function when building the application and, after filtering by the filter panel, it is passed to modules, wrapped in a reactive expression. The teal_data class allows modules to track the R code that they execute so that module outputs can be reproduced. See the teal.data package for a detailed explanation.

Example modules

Viewing data

Here is a minimal module that allows the user to select and view one dataset at a time. By default, filtering is enabled for all datasets. Note that dataset choices are specified by the datanames property of the teal_data container.

library(teal)

example_module <- function(label = "example teal module") {
  checkmate::assert_string(label)

  module(
    label = label,
    server = function(id, data) {
      checkmate::assert_class(data, "reactive")
      checkmate::assert_class(isolate(data()), "teal_data")

      moduleServer(id, function(input, output, session) {
        updateSelectInput(session, "dataname", choices = isolate(datanames(data())))
        output$dataset <- renderPrint({
          req(input$dataname)
          data()[[input$dataname]]
        })
      })
    },
    ui = function(id) {
      ns <- NS(id)
      sidebarLayout(
        sidebarPanel(selectInput(ns("dataname"), "Choose a dataset", choices = NULL)),
        mainPanel(verbatimTextOutput(ns("dataset")))
      )
    }
  )
}

Interacting with data and viewing code

The example below allows the user to interact with the data to create a simple visualization. In addition, it prints the code that can be used to reproduce that visualization.

library(teal)

# ui function for the module
# allows for selecting dataset and one of its numeric variables
ui_histogram_example <- function(id) {
  ns <- NS(id)
  sidebarLayout(
    sidebarPanel(
      selectInput(ns("datasets"), "select dataset", choices = NULL),
      selectInput(ns("numerics"), "select numeric variable", choices = NULL)
    ),
    mainPanel(
      plotOutput(ns("plot")),
      verbatimTextOutput(ns("code"))
    ),
  )
}

# server function for the module
# presents datasets and numeric variables for selection
# displays a histogram of the selected variable
# displays code to reproduce the histogram
srv_histogram_example <- function(id, data) {
  checkmate::assert_class(data, "reactive")
  checkmate::assert_class(isolate(data()), "teal_data")

  moduleServer(id, function(input, output, session) {
    # update dataset and variable choices
    # each selection stored in separate reactive expression
    updateSelectInput(inputId = "datasets", choices = isolate(datanames(data())))
    observe({
      req(dataset())
      nums <- vapply(data()[[dataset()]], is.numeric, logical(1L))
      updateSelectInput(inputId = "numerics", choices = names(nums[nums]))
    })
    dataset <- reactive(input$datasets)
    selected <- reactive(input$numerics)

    # add plot code
    plot_code_q <- reactive({
      validate(need(length(dataset()) == 1L, "Please select a dataset"))
      validate(need(length(selected()) == 1L, "Please select a variable"))
      req(selected() %in% names(data()[[dataset()]]))

      # evaluate plotting expression within data
      # inject input values into plotting expression
      within(
        data(),
        p <- hist(dataset[, selected], las = 1),
        dataset = as.name(dataset()), selected = selected()
      )
    })

    # view plot
    output$plot <- renderPlot({
      plot_code_q()[["p"]]
    })

    # view code
    output$code <- renderPrint({
      plot_code_q() %>%
        get_code() %>%
        cat()
    })
  })
}

# function that creates module instance to use in `teal` app
tm_histogram_example <- function(label) {
  module(
    label = label,
    server = srv_histogram_example,
    ui = ui_histogram_example,
    datanames = "all"
  )
}

This module is ready to be used in a teal app.

app <- init(
  data = teal_data(IRIS = iris, NPK = npk),
  modules = tm_histogram_example(label = "Histogram Module"),
  header = "Simple app with custom histogram module"
)

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

Teal Duck

Adding reporting to a module

Refer to this vignette to read about adding support for reporting in your teal module.

Using standard widgets in your custom module

The teal.widgets package provides various widgets which can be leveraged to quickly create standard elements in your custom module.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.