Defaults for all tracks

TL;DR: most track settings carry a push-pin beside them. Clicking it applies that value to every open track of the same type, and a snackbar then offers to keep it as the default for the ones you open later. An outline pin means "not the default", a filled one means it is — so a default takes two clicks, and clicking a filled pin clears it.

This is the in-app counterpart to the displayDefaults an administrator can bake into config.json (see display settings). Anyone can set these, and they last beyond the current session.

Applying a value to every open track#

Open the menu that offers the setting — the track menu, for most display types — find the setting, and click the pin on the row for the value you want. Every open track of that type takes the value — the ones you had already set individually included — and an "Applied to N open tracks" snackbar says how many.

✕

Do it yourselfIn DesktopSession specIn a notebookWith an agent

The steps behind the figure above, run against your own data.

1. Open your genome: on the JBrowse Desktop start screen click Open new genome (or Show all available genomes to pick a hosted one).This figure uses volvox, loaded from a .2bit genome.
2. Add your own track: File → Open track..., then paste a URL or choose a local file. This one needs a BAM file (.bam + .bai).This figure uses “volvox-sorted.bam (ctgA, canvas)”.
3. Add your own track: File → Open track..., then paste a URL or choose a local file. This one needs a CRAM file (.cram + .crai).This figure uses “volvox-sorted.cram (ctgA, default display)”.
4. Track menu → Read height → Custom... → 12px“volvox-sorted.cram (ctgA, default display)”.
5. Type your region of interest into the location box and press Enter.This figure is at ctgA:1..8,000.

Open this view in JBrowse Desktop ↗

Opens JBrowse Desktop (JBrowse Desktop 5.0+) at this view and saves it as a reopenable session — swap in your own files afterwards.

Nothing happens? Paste this link into Desktop's Open JBrowse Web link... (start screen, or File → Session):

Copy

https://jbrowse.org/code/jb2/main/?config=test_data%2Fvolvox%2Fconfig.json&session=spec-%7B%22views%22%3A%5B%7B%22type%22%3A%22LinearGenomeView%22%2C%22assembly%22%3A%22volvox%22%2C%22loc%22%3A%22ctgA%3A1..8%2C000%22%2C%22tracks%22%3A%5B%7B%22trackId%22%3A%22volvox_alignments_pileup_coverage%22%2C%22type%22%3A%22LinearAlignmentsDisplay%22%7D%2C%7B%22trackId%22%3A%22volvox_cram_alignments_ctga%22%2C%22type%22%3A%22LinearAlignmentsDisplay%22%2C%22featureHeight%22%3A12%7D%5D%7D%5D%7D&sessionName=JBrowse+docs%3A+feature_height_default

This session spec pastes after &session=spec- on any JBrowse Web instance.

Copy

{
  "views": [
    {
      "type": "LinearGenomeView",
      "assembly": "volvox",
      "loc": "ctgA:1..8,000",
      "tracks": [
        {
          "trackId": "volvox_alignments_pileup_coverage",
          "type": "LinearAlignmentsDisplay"
        },
        {
          "trackId": "volvox_cram_alignments_ctga",
          "type": "LinearAlignmentsDisplay",
          "featureHeight": 12
        }
      ]
    }
  ]
}

Loaded against config: test_data/volvox/config.json

The same view with jbrowse-anywidget. Point the adapter at your own file.

Copy

from jbrowse_anywidget import LinearGenomeView, make_assembly

view = LinearGenomeView(
    assembly=make_assembly("volvox", "https://your-server/your-genome.fa.gz"),
    location="ctgA:1..8,000",
)

view.add_track({
    "type": "AlignmentsTrack",
    "trackId": "my_track_1",
    "name": "My track 1",
    "assemblyNames": ["volvox"],
    "adapter": {"type": "BamAdapter", "uri": "https://your-server/your-file"},
})
view.add_track({
    "type": "AlignmentsTrack",
    "trackId": "my_track_2",
    "name": "My track 2",
    "assemblyNames": ["volvox"],
    "adapter": {"type": "CramAdapter", "uri": "https://your-server/your-file"},
})

view  # display the widget

Hand this to a coding agent. It rebuilds the figure above headlessly, and the session file is then the thing to edit — swap an adapter uri for your own file and rerun.

Copy

cat > session.json <<'JSON'
{
  "views": [
    {
      "type": "LinearGenomeView",
      "assembly": "volvox",
      "loc": "ctgA:1..8,000",
      "tracks": [
        {
          "trackId": "volvox_alignments_pileup_coverage",
          "type": "LinearAlignmentsDisplay"
        },
        {
          "trackId": "volvox_cram_alignments_ctga",
          "type": "LinearAlignmentsDisplay",
          "featureHeight": 12
        }
      ]
    }
  ]
}
JSON

npx @jbrowse/capture --instance https://jbrowse.org/code/jb2/main/ \
  --config https://jbrowse.org/code/jb2/main/test_data/volvox/config.json \
  --session session.json -o figure.png

Using JBrowse with AI agents covers the rest: hosted genomes to point it at, and why waiting for the render is the part that goes wrong.

Keeping it as the default#

The snackbar's Set as the default action is the second, deliberate step. It stores the value as your default for that display type, so tracks you open later start there too. The pin fills in to say the default is set.

Two things follow:

• The default only reaches tracks with no value of their own. The tracks the pin just wrote have one now, so a default you change later won't move them — click the new value's pin again.
• Choosing a value from a menu row, rather than from its pin, is a change to that one track.

Clicking a filled pin clears the default. It does not undo the values the pin wrote: those tracks keep what you applied, and only the tracks you open from then on go back to JBrowse's built-in value.

Defaults are keyed to the type of display rather than to all tracks at once. A read height default applies to your alignments tracks, a feature height default to your gene and feature tracks. Two track types that happen to share a setting name are independent.

How a setting is resolved#

Each setting is read in this order, first hit wins:

• the value set on that track, if it has one
• your default for that display type, if you have pinned one
• JBrowse's built-in value

Finding the tracks a default affects#

An open track whose appearance comes from a default is marked with a pencil in the track selector. It opens a dialog naming the setting, the built-in value, and what the track is showing now, with Clear session default to remove it. Closed tracks carry no marker, because nothing is being shown differently yet.

✕

Do it yourselfIn DesktopSession specIn a notebookWith an agent

The steps behind the figure above, run against your own data.

1. Open your genome: on the JBrowse Desktop start screen click Open new genome (or Show all available genomes to pick a hosted one).This figure uses volvox, loaded from a .2bit genome.
2. Add your own track: File → Open track..., then paste a URL or choose a local file. This one needs a BAM file (.bam + .bai).This figure uses “volvox-sorted.bam (ctgA, canvas)”.
3. Type your region of interest into the location box and press Enter.This figure is at ctgA:1..8,000.

Open this view in JBrowse Desktop ↗

Opens JBrowse Desktop (JBrowse Desktop 5.0+) at this view and saves it as a reopenable session — swap in your own files afterwards.

Nothing happens? Paste this link into Desktop's Open JBrowse Web link... (start screen, or File → Session):

Copy

https://jbrowse.org/code/jb2/main/?config=test_data%2Fvolvox%2Fconfig.json&session=spec-%7B%22views%22%3A%5B%7B%22type%22%3A%22LinearGenomeView%22%2C%22assembly%22%3A%22volvox%22%2C%22loc%22%3A%22ctgA%3A1..8%2C000%22%2C%22tracks%22%3A%5B%22volvox_alignments_pileup_coverage%22%5D%7D%5D%7D&sessionName=JBrowse+docs%3A+display_type_default_badge

This session spec pastes after &session=spec- on any JBrowse Web instance.

Copy

{
  "views": [
    {
      "type": "LinearGenomeView",
      "assembly": "volvox",
      "loc": "ctgA:1..8,000",
      "tracks": [
        "volvox_alignments_pileup_coverage"
      ]
    }
  ]
}

Loaded against config: test_data/volvox/config.json

The same view with jbrowse-anywidget. Point the adapter at your own file.

Copy

from jbrowse_anywidget import LinearGenomeView, make_assembly

view = LinearGenomeView(
    assembly=make_assembly("volvox", "https://your-server/your-genome.fa.gz"),
    location="ctgA:1..8,000",
)

view.add_track({
    "type": "AlignmentsTrack",
    "trackId": "my_track",
    "name": "My track",
    "assemblyNames": ["volvox"],
    "adapter": {"type": "BamAdapter", "uri": "https://your-server/your-file"},
})

view  # display the widget

Hand this to a coding agent. It rebuilds the figure above headlessly, and the session file is then the thing to edit — swap an adapter uri for your own file and rerun.

Copy

cat > session.json <<'JSON'
{
  "views": [
    {
      "type": "LinearGenomeView",
      "assembly": "volvox",
      "loc": "ctgA:1..8,000",
      "tracks": [
        "volvox_alignments_pileup_coverage"
      ]
    }
  ]
}
JSON

npx @jbrowse/capture --instance https://jbrowse.org/code/jb2/main/ \
  --config https://jbrowse.org/code/jb2/main/test_data/volvox/config.json \
  --session session.json -o figure.png

Using JBrowse with AI agents covers the rest: hosted genomes to point it at, and why waiting for the render is the part that goes wrong.

The same pencil marks a track you have edited directly. The tooltip and the dialog say which of the two it is, and a track affected by both lists them separately.

Reviewing all of your defaults#

Tools → Preferences → Reset to defaults... lists every preference that differs from its default, including one row per pinned default. Revert a single row with its revert button, or reset them all at once.

Where defaults are kept#

Pinned defaults are personal and are stored in your browser, or in the app in JBrowse Desktop. They are not part of the session, so they survive a reload and apply to the next session you open, and they are not included when you share one:

• A session you share or export records the values the tracks were actually showing, so whoever opens it sees the settings you had turned on even if they have pinned different defaults of their own.
• A setting you left at JBrowse's built-in value has nothing to record, so if the person opening it has pinned something there, theirs applies — the same way they view your session in their own theme.
• A track that recipient opens fresh in that session follows their defaults, as usual.
• Embedded components (@jbrowse/react-linear-genome-view2 and friends) have no preference storage, so a default set there lasts as long as the page.

Settings that offer a default#

Each setting below resolves through a session-wide default for its display type. Follow a link for what the setting does and what it falls back to when nothing is pinned.

The pin itself lives on the setting's own row, in whichever menu offers that setting, so you only meet it where the setting is. That is the track menu for most display types, but not all: a synteny view owns its ribbons, so Curved lines and Location markers and their pins are on the Synteny display settings button in the view header rather than on any one track's menu. Those two checkboxes write the setting on every synteny track the view shows, the same per-track write as any other checkbox here, so the pin beside them is still what makes a value the session-wide default. A row appears while it applies to what the track is drawing — line width on a line rendering, point size on a scatter, the sashimi options once sashimi arcs are on — and a display that borrows another display's settings but curates its own menu (the synteny display reuses the alignments ones) offers only the rows it lists.

Settings not listed here are per-track only. Making one of those persistent is a config edit.

See also#

• Display settings
• Configuring tracks
• User guide: Alignments track
• DISPLAY_TYPE_DEFAULTS.md — the promotable slots and CSS-style cascade behind the resolution order above, and how a default survives being serialized into a shared session