Comparing genomes: synteny and dotplots

library(JBrowseR)

JBrowseR() shows a single linear view. For anything comparative — synteny, dotplots, breakpoint-split — JBrowseRApp() drives the full JBrowse 2 app, and a views list describes what to open. Each entry is a list(type, init) spec, the same vocabulary JBrowse Web serializes into its ?session=spec-… URLs — a plain list, with no R builder in the way. The fields each init accepts come from the view’s state-model docs — see LinearSyntenyView — and the PAF track is a PAFAdapter.

The browser below is live — drag either genome to pan; the ribbon between them follows.

Linear synteny

Two volvox assemblies (one carries a deletion) are tied together by a PAF track and shown as a linear synteny view. Each assembly is a list(name=, uri=) that core expands; the PAF track spans both and so names them in order.

base <- "https://jbrowse.org/code/jb2/main/test_data/volvox/"

JBrowseRApp(
  assemblies = list(
    list(name = "volvox", uri = paste0(base, "volvox.2bit")),
    list(name = "volvox_del", uri = paste0(base, "volvox_del.fa"))
  ),
  tracks = list(
    list(
      type = "SyntenyTrack",
      trackId = "volvox_del_paf",
      name = "volvox_del.paf",
      assemblyNames = list("volvox", "volvox_del"),
      adapter = list(
        type = "PAFAdapter",
        targetAssembly = "volvox",
        queryAssembly = "volvox_del",
        uri = paste0(base, "volvox_del.paf")
      )
    )
  ),
  views = list(list(
    type = "LinearSyntenyView",
    init = list(
      views = list(list(assembly = "volvox"), list(assembly = "volvox_del")),
      tracks = list("volvox_del_paf")
    )
  ))
)

Dotplot

The same assemblies and PAF render as a dotplot with one field different — "DotplotView" in place of "LinearSyntenyView":

JBrowseRApp(
  assemblies = list(
    list(name = "volvox", uri = paste0(base, "volvox.2bit")),
    list(name = "volvox_del", uri = paste0(base, "volvox_del.fa"))
  ),
  tracks = list(
    list(
      type = "SyntenyTrack",
      trackId = "volvox_del_paf",
      name = "volvox_del.paf",
      assemblyNames = list("volvox", "volvox_del"),
      adapter = list(
        type = "PAFAdapter",
        targetAssembly = "volvox",
        queryAssembly = "volvox_del",
        uri = paste0(base, "volvox_del.paf")
      )
    )
  ),
  views = list(list(
    type = "DotplotView",
    init = list(
      views = list(list(assembly = "volvox"), list(assembly = "volvox_del")),
      tracks = list("volvox_del_paf")
    )
  ))
)