Editing a track's plot as text
Every track whose display has colour, grouping, rows, axis or filter settings has Advanced → Edit plot... in its track menu. It opens those settings as text, in the shape a config file writes them, so anything the menus and dialogs cannot express (a ramp, several threshold cuts, a typed section order, a filter expression) can be written directly. The Group by, Color by attribute and colour dialogs also open it from a button, filled in with the choice you have made there but not yet applied.
What the box shows
The text holds the current values of this display's settings. A setting at its default is left out, as it would be in a config file. Show help lists the settings, each with a line saying what it holds. Which settings appear depends on the display:
| Display | Settings |
|---|---|
| Feature, single-sample variant | facet, color, filter |
| Multi-row feature | facet, rows, rowColor, color |
| Multi-sample variant | facet, rows, rowColor, color, filter |
| Alignments, synteny in a genome view | facet, color, baseColor, arcColor, scales, filterBy |
| Quantitative | rows, rowColor, color, scales |
| Multiple alignment (MAF) | rows, rowColor, color |
| Hi-C | color |
| Multi-way synteny | color, ribbonColor, laneLayers |
| Mark plot, Manhattan | marks, transform, facet, rows, rowColor, scales, filter |
The Config reference link opens the display's page in the config reference, which spells out each setting's members.
Examples
The buttons above the text are worked examples for that display. A button fills the text with its example laid over the current settings, so you can read what it changes before applying it. For a feature track:
{ "facet": "strand", "color": { "field": "type" } }stacks one section per strand and colours each feature by its type.
Writing and applying
- A setting left out stays as it is.
- An object replaces the setting whole: a member you delete returns to its default.
nullresets a setting.- A string is a setting's one-value form, such as a facet's field or a constant colour.
The line under the text says which settings applying would set or reset, and Apply is disabled while the text is something the track's config would refuse, with the reason shown. A setting spelled another way but meaning the same thing changes nothing. Apply writes the settings onto the track, so they are kept with the session and Reset track settings returns them to the track's config.
From an agent or a script
The same settings are a display's plot: read display.plot, edit a copy,
check it with display.plotProblems(draft), and write it with
display.applyPlot(draft). See
Agents and the live model.