Using TreatmentPatterns' Shiny Modules

TreatmentPatterns provides several shiny modules. Shiny modules allow to quickly build a shiny app, based on pre-written code. In TreatmentPatterns there are 3 modules availible: 1) InputHandler, 2) InteractivePlots, and 3) CharacterizationPlots. These modules are represented as R6 classes.

Generic interface

Each module as 3 methods that represent the main interface on how to utilize them: 1) uiBody, 2) uiMenu, 3) server.

uiBody

The uiBody() method calls for the body of the module, which can be used inside a layout like fluidPage() from the shiny package or dashboardPage() from the shinydashboard package.

uiMenu

The uiMenu() method calls for a menu link which points toward the page generated by uiBody(). This is typically used with shinydashboard’s dashboardPage().

server

The server() method calls the back-end of the module, which handles all the internal computations, data filtering, and file management.

InputHandler

The InputHandler module has some key methods that can be used to setup your TreatmentPatterns shiny application quickly. First we need to create an object of the class InputHandler which we do like so:

library(TreatmentPatterns)

inputHandler <- InputHandler$new("app")

Now that our InputHandler is initialized and ready to go, we have access to the uiBody() and uiMenu() methods to build our UI with. In this example the uiMenu() is wrapped inside sidebarMenu() and dashboardSidebar(). The uiBody() method is wrapped inside tabItems() and dashboardBody().

library(shiny)
library(shinydashboard)

inputHandler <- InputHandler$new("app")

ui <- dashboardPage(
  header = dashboardHeader(title = "myApp"),
  sidebar = dashboardSidebar(sidebarMenu(
    # InputHandler menu item
    inputHandler$uiMenu(),
    
    # Database Selection
    inputHandler$uiDatabaseSelector()
  )),
  body = dashboardBody(tabItems(
    # InputHandler body
    inputHandler$uiBody()
  ))
)

We also have access to the setDataPath() and server() methods. The setDataPath() method allows us to specify either a path to a zip-file, or pass the input from our server function.

When we set the path parameter instead, the input becomes static. Note, that this also renders the uiBody() and uiMenu() methods redundant.

server <- function(input, output, session) {
  shiny::moduleServer("app", function(input, output, session) {
    # Set static path
    inputHandler$setDataPath(path = system.file(package = "TreatmentPatterns", "DummyOutput", "output.zip"))
    # Run server back-end
    inputHandler$server(input, output, session)
  })
}

shinyApp(ui, server)

If we pass the input, the user can interactively upload a zip file.

# Data uploaded by user
server <- function(input, output, session) {
  shiny::moduleServer("app", function(input, output, session) {
    # Set input, for interactive file upload
    inputHandler$setDataPath(input = input)
    # InputHandler back-end
    inputHandler$server(input, output, session)
  })
}

InteractivePlots

Lets first create an InteractivePlots module object.

sunburstPlot <- SunburstPlot$new("app")
sankeyDiagram <- SankeyDiagram$new("app")

We can now add our UI by calling the uiMenu() and uiBody() methods.

ui <- dashboardPage(
  header = dashboardHeader(title = "myApp"),
  sidebar = dashboardSidebar(sidebarMenu(
    # InputHandler menu item
    inputHandler$uiMenu(),
    
    # InteractivePlots menu item
    sunburstPlot$uiMenu(),
    sankeyDiagram$uiMenu(),
    
    # Database Selection
    inputHandler$uiDatabaseSelector()
  )),
  body = dashboardBody(tabItems(
    # InputHandler body
    inputHandler$uiBody(),
    
    # InteractivePlots body
    sunburstPlot$uiBody(),
    sankeyDiagram$uiBody()
  ))
)

Finally we can add our server back-end to the server function. Note that the server() method for InteractivePlots also takes the inputHandler module object as an input.

server <- function(input, output, session) {
  shiny::moduleServer("app", function(input, output, session) {
    # Set input, for interactive file upload
    inputHandler$setDataPath(path = system.file(package = "TreatmentPatterns", "DummyOutput", "output.zip"))
    # InputHandler back-end
    inputHandler$server(input, output, session)
    
    # InteracitvePlots back-end
    sunburstPlot$server(input, output, session, inputHandler)
    sankeyDiagram$server(input, output, session, inputHandler)
  })
}

shinyApp(ui, server)

CharacterizationPlots

Lets first create an CharacterizationPlots module object.

characterizationPlots <- CharacterizationPlots$new("app")

We can now add our UI by calling the uiMenu() and uiBody() methods.

ui <- dashboardPage(
  header = dashboardHeader(title = "myApp"),
  sidebar = dashboardSidebar(sidebarMenu(
    # InputHandler menu item
    inputHandler$uiMenu(),
    
    # InteractivePlots menu item
    sunburstPlot$uiMenu(),
    sankeyDiagram$uiMenu(),
    
    # CharacterizationPlots menu item
    characterizationPlots$uiMenu(),
    
    # Database Selection
    inputHandler$uiDatabaseSelector()
  )),
  body = dashboardBody(tabItems(
    # InputHandler body
    inputHandler$uiBody(),
    
    # InteractivePlots body
    sunburstPlot$uiBody(),
    sankeyDiagram$uiBody(),
    
    # CharacterizationPlots body
    characterizationPlots$uiBody()
  ))
)

Finally we can add our server back-end to the server function. Note that the server() method for InteractivePlots also takes the inputHandler module object as an input.

server <- function(input, output, session) {
  shiny::moduleServer("app", function(input, output, session) {
    # Set input, for interactive file upload
    inputHandler$setDataPath(path = system.file(package = "TreatmentPatterns", "DummyOutput", "output.zip"))
    # InputHandler back-end
    inputHandler$server(input, output, session)
    
    # InteractivePlots back-end
    interactivePlots$server(input, output, session, inputHandler)
    
    # CharacterizationPlots back-end
    characterizationPlots$server(input, output, session, inputHandler)
  })
}

shinyApp(ui, server)