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

Source: R/app.R

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. Each views entry is a list(type = ..., init = ...) spec — the same vocabulary JBrowse Web serializes into its ?session=spec-… URLs — built most easily with linear_view(), synteny_view(), and dotplot_view().

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

Arguments

assemblies

A list of assembly configs (each from assembly(), or a plain config list). A synteny/dotplot view needs two or more.

tracks

A list of full track config lists. Because a synteny track spans two assemblies there is no single-assembly shorthand; synteny_track() builds the common PAF case.

views

A list of view specs, e.g. from synteny_view() / linear_view().

plugins

A list of JBrowse plugin specs (name + url) to load at runtime.

theme

A theme config from theme().

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

Examples

if (FALSE) { # \dontrun{
JBrowseRApp(
  assemblies = list(assembly(hg38_fa), assembly(mm39_fa)),
  tracks = list(synteny_track(paf_url, "hg38", "mm39")),
  views = list(synteny_view(c("hg38", "mm39"), tracks = "hg38-mm39"))
)
} # }