# 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](https://jbrowse.org/jb2/docs/tutorials/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.

<Figure caption="Applying Compact as the read height. Top: the pin on the Compact preset. Bottom: both open alignments tracks are compact, and the snackbar offers to keep Compact as the default." src="/img/feature_height_default.png" />

## 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.

<Figure caption="After pinning Compact, the alignments track carries a pencil in the track selector. The dialog it opens lists featureHeight under 'Session-wide default', and offers to clear it." src="/img/display_type_default_badge.png" />

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.

<!-- PROMOTABLE_SLOTS START -->

<!-- prettier-ignore -->
| Track type | Display | Settings with a session-wide default |
| --- | --- | --- |
| VariantTrack | [](https://jbrowse.org/jb2/docs/config/lddisplay) | [`showLegend`](https://jbrowse.org/jb2/docs/config/lddisplay/#slot-showlegend) |
| LDTrack | [](https://jbrowse.org/jb2/docs/config/ldtrackdisplay) | [`showLegend`](https://jbrowse.org/jb2/docs/config/ldtrackdisplay/#slot-showlegend) |
| SyntenyTrack | [](https://jbrowse.org/jb2/docs/config/lgvsyntenydisplay) | [`colorBy`](https://jbrowse.org/jb2/docs/config/lgvsyntenydisplay/#slot-colorby), [`featureHeight`](https://jbrowse.org/jb2/docs/config/lgvsyntenydisplay/#slot-featureheight), [`heightMode`](https://jbrowse.org/jb2/docs/config/lgvsyntenydisplay/#slot-heightmode), [`hideNonCanonicalJunctions`](https://jbrowse.org/jb2/docs/config/lgvsyntenydisplay/#slot-hidenoncanonicaljunctions), [`linkedReads`](https://jbrowse.org/jb2/docs/config/lgvsyntenydisplay/#slot-linkedreads), [`mismatchAlpha`](https://jbrowse.org/jb2/docs/config/lgvsyntenydisplay/#slot-mismatchalpha), [`readConnections`](https://jbrowse.org/jb2/docs/config/lgvsyntenydisplay/#slot-readconnections), [`readConnectionsDown`](https://jbrowse.org/jb2/docs/config/lgvsyntenydisplay/#slot-readconnectionsdown), [`sashimiArcsMode`](https://jbrowse.org/jb2/docs/config/lgvsyntenydisplay/#slot-sashimiarcsmode), [`showLegend`](https://jbrowse.org/jb2/docs/config/lgvsyntenydisplay/#slot-showlegend), [`showSashimiArcs`](https://jbrowse.org/jb2/docs/config/lgvsyntenydisplay/#slot-showsashimiarcs), [`showSashimiLabels`](https://jbrowse.org/jb2/docs/config/lgvsyntenydisplay/#slot-showsashimilabels), [`showSoftClipping`](https://jbrowse.org/jb2/docs/config/lgvsyntenydisplay/#slot-showsoftclipping) |
| AlignmentsTrack | [](https://jbrowse.org/jb2/docs/config/linearalignmentsdisplay) | [`colorBy`](https://jbrowse.org/jb2/docs/config/linearalignmentsdisplay/#slot-colorby), [`featureHeight`](https://jbrowse.org/jb2/docs/config/linearalignmentsdisplay/#slot-featureheight), [`heightMode`](https://jbrowse.org/jb2/docs/config/linearalignmentsdisplay/#slot-heightmode), [`hideNonCanonicalJunctions`](https://jbrowse.org/jb2/docs/config/linearalignmentsdisplay/#slot-hidenoncanonicaljunctions), [`linkedReads`](https://jbrowse.org/jb2/docs/config/linearalignmentsdisplay/#slot-linkedreads), [`mismatchAlpha`](https://jbrowse.org/jb2/docs/config/linearalignmentsdisplay/#slot-mismatchalpha), [`readConnections`](https://jbrowse.org/jb2/docs/config/linearalignmentsdisplay/#slot-readconnections), [`readConnectionsDown`](https://jbrowse.org/jb2/docs/config/linearalignmentsdisplay/#slot-readconnectionsdown), [`sashimiArcsMode`](https://jbrowse.org/jb2/docs/config/linearalignmentsdisplay/#slot-sashimiarcsmode), [`showLegend`](https://jbrowse.org/jb2/docs/config/linearalignmentsdisplay/#slot-showlegend), [`showSashimiArcs`](https://jbrowse.org/jb2/docs/config/linearalignmentsdisplay/#slot-showsashimiarcs), [`showSashimiLabels`](https://jbrowse.org/jb2/docs/config/linearalignmentsdisplay/#slot-showsashimilabels), [`showSoftClipping`](https://jbrowse.org/jb2/docs/config/linearalignmentsdisplay/#slot-showsoftclipping) |
| FeatureTrack | [](https://jbrowse.org/jb2/docs/config/linearbasicdisplay) | [`displayDirectionalChevrons`](https://jbrowse.org/jb2/docs/config/linearbasicdisplay/#slot-displaydirectionalchevrons), [`displayMode`](https://jbrowse.org/jb2/docs/config/linearbasicdisplay/#slot-displaymode), [`heightMode`](https://jbrowse.org/jb2/docs/config/linearbasicdisplay/#slot-heightmode), [`showLabels`](https://jbrowse.org/jb2/docs/config/linearbasicdisplay/#slot-showlabels), [`showLegend`](https://jbrowse.org/jb2/docs/config/linearbasicdisplay/#slot-showlegend), [`subfeatureLabels`](https://jbrowse.org/jb2/docs/config/linearbasicdisplay/#slot-subfeaturelabels) |
| ReferenceSequenceTrack | [](https://jbrowse.org/jb2/docs/config/lineargccontentdisplay) | [`lineWidth`](https://jbrowse.org/jb2/docs/config/lineargccontentdisplay/#slot-linewidth), [`scatterPointSize`](https://jbrowse.org/jb2/docs/config/lineargccontentdisplay/#slot-scatterpointsize) |
| GCContentTrack | [](https://jbrowse.org/jb2/docs/config/lineargccontenttrackdisplay) | [`lineWidth`](https://jbrowse.org/jb2/docs/config/lineargccontenttrackdisplay/#slot-linewidth), [`scatterPointSize`](https://jbrowse.org/jb2/docs/config/lineargccontenttrackdisplay/#slot-scatterpointsize) |
| HicTrack | [](https://jbrowse.org/jb2/docs/config/linearhicdisplay) | [`showLegend`](https://jbrowse.org/jb2/docs/config/linearhicdisplay/#slot-showlegend) |
| GWASTrack | [](https://jbrowse.org/jb2/docs/config/linearmanhattandisplay) | [`scatterPointSize`](https://jbrowse.org/jb2/docs/config/linearmanhattandisplay/#slot-scatterpointsize), [`showLdLegend`](https://jbrowse.org/jb2/docs/config/linearmanhattandisplay/#slot-showldlegend) |
| FeatureTrack | [](https://jbrowse.org/jb2/docs/config/linearmultirowfeaturedisplay) | [`showLegend`](https://jbrowse.org/jb2/docs/config/linearmultirowfeaturedisplay/#slot-showlegend) |
| VariantTrack | [](https://jbrowse.org/jb2/docs/config/linearmultisamplevariantdisplay) | [`showLegend`](https://jbrowse.org/jb2/docs/config/linearmultisamplevariantdisplay/#slot-showlegend) |
| VariantTrack | [](https://jbrowse.org/jb2/docs/config/linearmultisamplevariantmatrixdisplay) | [`showLegend`](https://jbrowse.org/jb2/docs/config/linearmultisamplevariantmatrixdisplay/#slot-showlegend) |
| VariantTrack | [](https://jbrowse.org/jb2/docs/config/linearpairedarcdisplay) | [`lineWidth`](https://jbrowse.org/jb2/docs/config/linearpairedarcdisplay/#slot-linewidth) |
| SyntenyTrack | [](https://jbrowse.org/jb2/docs/config/linearsyntenydisplay) | [`drawCurves`](https://jbrowse.org/jb2/docs/config/linearsyntenydisplay/#slot-drawcurves), [`drawLocationMarkers`](https://jbrowse.org/jb2/docs/config/linearsyntenydisplay/#slot-drawlocationmarkers) |
| VariantTrack | [](https://jbrowse.org/jb2/docs/config/linearvariantdisplay) | [`displayDirectionalChevrons`](https://jbrowse.org/jb2/docs/config/linearvariantdisplay/#slot-displaydirectionalchevrons), [`displayMode`](https://jbrowse.org/jb2/docs/config/linearvariantdisplay/#slot-displaymode), [`heightMode`](https://jbrowse.org/jb2/docs/config/linearvariantdisplay/#slot-heightmode), [`showLabels`](https://jbrowse.org/jb2/docs/config/linearvariantdisplay/#slot-showlabels), [`showLegend`](https://jbrowse.org/jb2/docs/config/linearvariantdisplay/#slot-showlegend), [`subfeatureLabels`](https://jbrowse.org/jb2/docs/config/linearvariantdisplay/#slot-subfeaturelabels) |
| QuantitativeTrack | [](https://jbrowse.org/jb2/docs/config/linearwiggledisplay) | [`lineWidth`](https://jbrowse.org/jb2/docs/config/linearwiggledisplay/#slot-linewidth), [`scatterPointSize`](https://jbrowse.org/jb2/docs/config/linearwiggledisplay/#slot-scatterpointsize) |
| MultiQuantitativeTrack | [](https://jbrowse.org/jb2/docs/config/multilinearwiggledisplay) | [`lineWidth`](https://jbrowse.org/jb2/docs/config/multilinearwiggledisplay/#slot-linewidth), [`scatterPointSize`](https://jbrowse.org/jb2/docs/config/multilinearwiggledisplay/#slot-scatterpointsize), [`showLegend`](https://jbrowse.org/jb2/docs/config/multilinearwiggledisplay/#slot-showlegend) |

<!-- PROMOTABLE_SLOTS END -->

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

## See also

- [](https://jbrowse.org/jb2/docs/tutorials/display_settings)
- [Configuring tracks](https://jbrowse.org/jb2/docs/config_guides/tracks)
- [](https://jbrowse.org/jb2/docs/user_guides/alignments_track)
- [DISPLAY_TYPE_DEFAULTS.md](https://github.com/GMOD/jbrowse-components/blob/main/agent-docs/reference/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