Embed the full JBrowse 2 app (multiple views of any type)

Where JBrowseR() shows a single linear genome view, JBrowseRApp() drives the whole app engine, so views can mix a linear view, a synteny view, a dotplot, and more.

JBrowseRApp(
  assemblies = NULL,
  tracks = NULL,
  views = NULL,
  session = NULL,
  plugins = NULL,
  theme = NULL,
  config = NULL,
  width = NULL,
  height = NULL,
  elementId = NULL
)

Arguments

assemblies: A list of assembly configs — list(name = , uri = ) each. A synteny/dotplot view needs two or more.
tracks: A list of full track config lists. A synteny track spans two assemblies, so it names both in assemblyNames and in its adapter.
views: A list of list(type = , init = ) view specs.
session: A previously saved session to restore instead of views — the value a running app reported as input[[paste0(outputId, "_session")]]. Unlike views, which describes what to open, this carries the state the user built: navigation, open tracks, per-display settings, widgets. views still describes what File → New session returns to.
plugins: A list of JBrowse plugin specs (name + url) to load at runtime.
theme: A theme config, the MUI palette JBrowse takes.
config: Escape hatch: a whole JBrowse config forming the payload base that explicit arguments override — a list, or the path, URL, or JSON text of a config.json.
width, height, elementId: Standard htmlwidget sizing arguments.

Value

an htmlwidget of the JBrowse 2 app

Details

Each views entry is a list(type = ..., init = ...) spec — the same vocabulary JBrowse Web serializes into its ?session=spec-… URLs, and the init fields are that view's own state-model options. There is no R constructor for it, so every view type JBrowse has — including one a runtime plugins entry registers — opens with nothing added to this package.

A comparative view's panels are list(assembly = , loc = ), one per side. Note that fields JBrowse reads as arrays need list(), since a length-1 vector would serialize as a JSON scalar.

Examples

if (FALSE) { # \dontrun{
JBrowseRApp(
  assemblies = list(
    list(name = "hg38", uri = hg38_fa),
    list(name = "mm39", uri = mm39_fa)
  ),
  tracks = list(list(
    type = "SyntenyTrack",
    trackId = "hg38_mm39",
    name = "hg38 vs mm39",
    assemblyNames = list("hg38", "mm39"),
    adapter = list(
      type = "PAFAdapter",
      targetAssembly = "hg38",
      queryAssembly = "mm39",
      uri = paf_url
    )
  )),
  views = list(list(
    type = "LinearSyntenyView",
    init = list(
      views = list(list(assembly = "hg38"), list(assembly = "mm39")),
      tracks = list("hg38_mm39")
    )
  ))
)
} # }