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

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

JBrowseRApp(
  ...,
  local_files = NULL,
  width = NULL,
  height = NULL,
  elementId = NULL
)

Arguments

...

createApp options, each named.

local_files

Files on this machine to open without a web server: a path, a vector of paths, or a list mixing paths with raw vectors. Each registers under its basename (or its list name), and a track refers to that name as if it were a URL. A sibling index (.tbi, .csi, .bai, .crai, .fai, .gzi) next to a path comes along.

width, height, elementId

Standard htmlwidget sizing arguments.

Value

an htmlwidget

Details

Every named argument in ... is an option of JBrowse's createApp, sent verbatim under JBrowse's own camelCase name: assemblies, tracks, views, session, connections, internetAccounts, aggregateTextSearchAdapters, configuration, plugins, and whatever JBrowse adds next. A whole options object is do.call(JBrowseRApp, jsonlite::read_json("options.json")).

A views entry is list(type = , ...) with the view's settings beside type, the object a config.json's defaultSession.views holds. An assemblies entry may be a hub name or sequence-file URL, as JBrowseR()'s assembly takes.

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",
    views = list(list(assembly = "hg38"), list(assembly = "mm39")),
    tracks = list("hg38_mm39")
  ))
)
} # }