Renders an interactive, GPU-accelerated JBrowse 2 linear genome view as an htmlwidget for R Markdown documents, Shiny apps, or the R console.
JBrowseR(
...,
local_files = NULL,
width = NULL,
height = NULL,
elementId = NULL
)createLinearGenomeView options, each named.
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.
Standard htmlwidget sizing arguments.
an htmlwidget
Every named argument in ... is an option of JBrowse's
createLinearGenomeView,
sent verbatim under JBrowse's own camelCase name: assembly, tracks,
location, session, aggregateTextSearchAdapters, internetAccounts,
plugins, configuration, and whatever JBrowse adds next. This package
names none of them, so a whole options object is
do.call(JBrowseR, jsonlite::read_json("options.json")).
assembly takes a hub name ("hg38", a GenArk accession), a sequence-file
URL, or an assembly config. A tracks entry takes a bare data-file URL, a
list(uri = ), a track_data_frame() result, or a full track config.
plugins entries are list(name = , url = ).
A length-1 vector serializes to a JSON scalar, so fields JBrowse reads as
arrays take list(): assemblyNames = list("hg38").
JBrowseR(assembly = "hg38", location = "BRCA1")