createLandingPage {iSEE} | R Documentation

## Create a landing page

### Description

Define a function to create a landing page in which users can specify or upload SummarizedExperiment objects.

### Usage

    createLandingPage(
      seUI = NULL,
      seLoad = NULL,
      initUI = NULL,
      initLoad = NULL,
      requireButton = TRUE
    )

### Arguments

`seUI` | Function that accepts a single `id` argument and returns a UI element for specifying the SummarizedExperiment.
`seLoad` | Function that accepts the input value of the UI element from `seUI` and returns a SummarizedExperiment object.
`initUI` | Function that accepts a single `id` argument and returns a UI element for specifying the initial state.
`initLoad` | Function that accepts the input value of the UI element from `initUI` and returns a list of Panels.
`requireButton` | Logical scalar indicating whether the app should require an explicit button press to initialize, or if it should initialize upon any modification to the UI element in `seUI`.

### Details

By default, this function creates a landing page in which users can upload an RDS file containing a SummarizedExperiment, which is subsequently read by `readRDS` to launch an instance of `iSEE`. However, any source of SummarizedExperiment objects can be used; for example, we can retrieve them from databases by modifying `seUI` and `seLoad` appropriately.

The default landing page also allows users to upload a RDS file containing a list of Panels that specifies the initial state of the `iSEE` instance (to be used as the `initial` argument in `iSEE`). Again, any source can be used to create this list if `initUI` and `initLoad` are modified appropriately.

The UI elements for the SummarizedExperiment and the initial state are named `"se"` and `"initial"` respectively. This can be used in Shiny bookmarking to initialize an `iSEE` in a desired state by simply clicking a link, provided that `requireButton=FALSE` so that reactive expressions are immediately triggered upon setting `se=` and `initial=` in the URL. We do not use bookmarking to set all individual `iSEE` parameters as we will run afoul of URL character limits.

### Value

A function that generates a landing page upon being passed to `iSEE` as the `landingPage` argument.

### Defining a custom landing page

We note that `createLandingPage` is just a limited wrapper around the landing page API. In `iSEE`, `landingPage` can be any function that accepts the following arguments:

- `FUN`, a function to initialize the `iSEE` observer architecture. This function expects to be passed:

  - `SE`, a SummarizedExperiment object.

  - `INITIAL`, a list of Panel objects describing the initial application state. If `NULL`, the initial state from `initial` in the top-level `iSEE` call is used instead.

  - `TOUR`, a data.frame containing a tour to be attached to the app - see `defaultTour` for an example. If `NULL` (the default), no tour is added.

- `input`, the Shiny input list.

- `output`, the Shiny output list.

- `session`, the Shiny session object.

The `landingPage` function should define a `renderUI` expression that is assigned to `output$allPanels`. This should define a UI that contains all widgets necessary for a user to set up an `iSEE` session interactively. We suggest that all UI elements have IDs prefixed with `"initialize_INTERNAL"` to avoid conflicts.

The function should also define observers to respond to user interactions with the UI elements. These are typically used to define a SummarizedExperiment object and an input state as a list of Panels; any one of these observers may then call `FUN` on those arguments to launch the main `iSEE` instance.

Note that, once the main app is launched, the UI elements constructed here are lost and observers will never be called again. There is no explicit “unload” mechanism to return to the landing page from the main app, though a browser refresh is usually sufficient.

### Author(s)

Aaron Lun

### Examples

    createLandingPage()

    # Alternative approach, to create a landing page
    # that opens one of the datasets from the scRNAseq package.
    library(scRNAseq)
    all.data <- ls("package:scRNAseq")
    all.data <- all.data[grep("Data$", all.data)]

    lpfun <- createLandingPage(
        seUI=function(id) selectInput(id, "Dataset:", choices=all.data),
        seLoad=function(x) get(x, as.environment("package:scRNAseq"))()
    )

    app <- iSEE(landingPage=lpfun)
    if (interactive()) {
      shiny::runApp(app, port=1234)
    }

[Package iSEE version 2.6.0 Index]