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, built with linear_view(),
synteny_view(), or dotplot_view(). 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.
Two volvox assemblies (one carries a deletion) are tied
together by a PAF track and shown as a linear synteny view.
assembly() handles the .2bit and FASTA
sequences; synteny_track() builds the PAF track that spans
both.
base <- "https://jbrowse.org/code/jb2/main/test_data/volvox/"
JBrowseRApp(
assemblies = list(
assembly(paste0(base, "volvox.2bit"), name = "volvox"),
assembly(paste0(base, "volvox_del.fa"), name = "volvox_del")
),
tracks = list(
synteny_track(paste0(base, "volvox_del.paf"), "volvox", "volvox_del",
track_id = "volvox_del_paf")
),
views = list(synteny_view(c("volvox", "volvox_del"), tracks = "volvox_del_paf"))
)The same assemblies and PAF render as a dotplot with one function
call different — dotplot_view() in place of
synteny_view():
JBrowseRApp(
assemblies = list(
assembly(paste0(base, "volvox.2bit"), name = "volvox"),
assembly(paste0(base, "volvox_del.fa"), name = "volvox_del")
),
tracks = list(
synteny_track(paste0(base, "volvox_del.paf"), "volvox", "volvox_del",
track_id = "volvox_del_paf")
),
views = list(dotplot_view(c("volvox", "volvox_del"), tracks = "volvox_del_paf"))
)