Package 'JBrowseR'

Description

Renders an interactive, GPU-accelerated JBrowse 2 linear genome view as an htmlwidget for R Markdown documents, Shiny apps, or the R console.

Usage

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

Arguments

Details

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").

Value

an htmlwidget

Examples

JBrowseR(assembly = "hg38", location = "BRCA1")

Description

Output and render functions for JBrowseR() in Shiny apps and interactive Rmd documents.

Usage

JBrowseROutput(outputId, width = "100%", height = "400px")

renderJBrowseR(expr, env = parent.frame(), quoted = FALSE)

Arguments

Details

The widget reports three inputs, namespaced by output id: input[[paste0(outputId, "_selected_feature")]] is the clicked feature, ⁠_location⁠ the visible region as the location box prints it (thousands separators included), and ⁠_session⁠ the layout in the shape ⁠session =⁠ takes. Each settles after a gesture rather than firing per frame.

A re-render whose options differ only in tracks, location or local_files is applied to the browser on the page, keeping the user's zoom and track order; any other changed option builds a new browser. Reading ⁠_location⁠ or ⁠_session⁠ in the reactive that feeds renderJBrowseR() builds a loop: navigate from an observer with update_jbrowse() instead.

Value

the Shiny UI bindings for a JBrowseR htmlwidget

the Shiny server bindings for a JBrowseR htmlwidget

Description

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.

Usage

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

Arguments

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.

Value

an htmlwidget

Examples

## Not run: 
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")
  ))
)

## End(Not run)

Description

Output and render functions for JBrowseRApp(). The app is a separate widget with its own bundle, so it cannot render into a JBrowseROutput().

Usage

JBrowseRAppOutput(outputId, width = "100%", height = "400px")

renderJBrowseRApp(expr, env = parent.frame(), quoted = FALSE)

Arguments

Details

The app reports input[[paste0(outputId, "_session")]] in the shape ⁠session =⁠ takes, ⁠_selected_feature⁠ for the clicked feature, and ⁠_location⁠ as a list with one entry per open view. A re-render that changes only session restores it in the app on the page; any other changed option builds a new app.

Value

the Shiny UI bindings for a JBrowseRApp htmlwidget

the Shiny server bindings for a JBrowseRApp htmlwidget

Description

Turns a data frame of features into an in-browser track (a FromConfigAdapter), no files or web server required. This is the natural way to view results you computed in R — peaks, windows, hits — directly on the genome.

Usage

track_data_frame(data, name, assembly_name = NULL, ...)

Arguments

Value

a track config list

Examples

df <- data.frame(
  chrom = c("1", "2"),
  start = c(123, 456),
  end = c(789, 101112),
  name = c("feature1", "feature2")
)
track_data_frame(df, "my_features")

# a point per row at its log2 fold-change, coloured by call
de <- data.frame(
  chrom = "7", start = c(1e6, 2e6), end = c(1e6, 2e6) + 6000,
  log2fc = c(2.1, -1.7), sig = c("up", "down")
)
track_data_frame(de, "de", displays = list(list(
  type = "LinearMarkDisplay",
  marks = list(list(
    mark = "point",
    encoding = list(y = "log2fc", color = list(field = "sig", scale = "categorical"))
  ))
)))

Description

Sends option changes to a JBrowseR() or JBrowseRApp() already on the page, without re-running its render expression. The changes are named the way the widget's own options are.

Usage

update_jbrowse(outputId, ..., domain = shiny_domain())

Arguments

Details

observeEvent(input$gene, update_jbrowse("browser", location = input$gene))

A JBrowseR() applies tracks and location in place and a JBrowseRApp() applies session in place; any other option builds a new browser from the rendered options plus the changes. A later re-render compares against what it rendered last, so a change sent here survives a re-render that does not restate that option.

Value

outputId, invisibly.