In seandavi/BiocGadgets: Shiny Gadgets for Bioconductor

knitr::opts_chunk$set(echo = TRUE)

Shiny

• interactively communicating ideas and results
  • plots
  • data
  • model fitting
• for full application development
  • interact with data sources
  • collect and react to input
  • ...

---

Gadgets vs Apps

• Gadgets are interactive tools that enhance the developer analyst experience
• Apps represent the output of an analsys, Gadgets are for using during an analysis
• The audience for an App is the end user, while the audience for a Gadget is an R user
• Gadget fundamentals are shiny, but design is focused
  • on limited screen space
  • on useful functionality during analysis
  • performing a function or returning results
• Apps run on Shiny Server, while Gadgets are intended to be invoked in code

---

Gadgets

Shiny Gadgets could be created for most any task you might do during data loading, cleaning, manipulation, and visualization.

• A tool to preview regular expressions for find/replace (sub and gsub)
• Visual selection tools for subsetting or outlier exclusion
• An easy-to-use UI for downloading data from a complicated API and turning it into a data frame
• ...

---

Gadget structure

library(shiny)
library(miniUI)

myGadgetFunc <- function(inputValue1, inputValue2) {
  ui <- miniPage(
    ## Define layout, inputs, outputs, etc.
  )

  server <- function(input, output, session) {
    # Define reactive expressions, outputs, etc.
    # And then 
    stopApp(returnValue)
  }
  runGadget(ui, server)
}

Gadget UI block

  ui <- miniPage(
    gadgetTitleBar("My Gadget"),
    miniContentPanel(
      # Define layout, inputs, outputs
    )
  )

---

Gadget Server block

  server <- function(input, output, session) {
    # Define reactive expressions, outputs, etc.

    # When the Done button is clicked, return a value
    observeEvent(input$done, {
      returnValue <- ...
      stopApp(returnValue)
    })
  }

regex test example

regexTest = function(pattern="night", 
                     x = "We can turn day into night with this Gadget",
                     replace = "day") {

  ui = miniPage(
    gadgetTitleBar("Basic gsub tester"),
    miniContentPanel(
      textInput("text","Text:", x),
      textInput('pattern','Pattern to replace:', pattern),
      textInput("replacement","Text to substitute", replace),
      textOutput("out")
    )
  )

  server = function(input, output, session) {
    output$out = renderText( gsub(pattern = input$pattern,
                                 replace = input$replacement, 
                                 x = input$text) )
    observeEvent(input$done, {
      returnValue <- input$pattern
      stopApp(returnValue)
    })
  }
  runGadget(ui, server)
}

---

ggbrush example

ggbrush <- function(dframe, xvar, yvar, viewer=paneViewer()) {

  ui <- miniPage(
    gadgetTitleBar("Drag to select points"),
    miniContentPanel(
      # The brush="brush" argument means we can listen for
      # brush events on the plot using input$brush.
      plotOutput("plot", height = "100%", brush = "brush")
    )
  )

  server <- function(input, output, session) {

    # Render the plot
    output$plot <- renderPlot({
      # Plot the data with x/y vars indicated by the caller.
      ggplot(dframe, aes_string(xvar, yvar)) + geom_point()
    })

    # Handle the Done button being pressed.
    observeEvent(input$done, {
      # Return the brushed points. See ?shiny::brushedPoints.
      stopApp(brushedPoints(dframe, input$brush))
    })
  }

  runGadget(ui, server)
}

---

Wrapping shiny

shinyFunction = function() {
  require(shiny)
  server <- function(input, output) {
    output$distPlot <- renderPlot({
      hist(rnorm(input$obs), col = 'darkgray', border = 'white')
    })
  }

  ui <- fluidPage(
    sidebarLayout(
      sidebarPanel(
        sliderInput("obs", "Number of observations:", min = 10, max = 500, value = 100)
      ),
      mainPanel(plotOutput("distPlot"))
    )
  )

  shinyApp(ui = ui, server = server)
}

---

Complex Shiny Wrap

shinyFunction = function() {
  runApp(system.file("MyPackage","shinyAppDir"))
}

---

Further reading

• http://shiny.rstudio.com/articles/gadget-ui.html
• http://shiny.rstudio.com/articles/plot-interaction.html
• https://github.com/rstudio/miniui
• https://github.com/seandavi/BiocGadgets

seandavi/BiocGadgets documentation built on May 29, 2019, 4:27 p.m.