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YChannel

Auto-generated from the config schema in the source — see the config guide for concepts. Built into JBrowse core. View source.

A value axis written as Vega-Lite's encoding.y: its scale, the axis guide it draws, and rules, reference lines at chosen values across every band the scale rules. A rule naming no color draws in the one color the chrome rules every plot in. The wiggle display's also names the field it plots (YFieldChannel).

Example usage

A log depth axis floored at 1, with a labelled line at 30x:

{
  type: 'LinearAlignmentsDisplay',
  coverage: {
    encoding: {
      y: {
        scale: { type: 'log', domainMin: 1 },
        rules: [{ value: 30, label: '30x' }],
      },
    },
  },
}

A titled Manhattan axis with a labelled genome-wide threshold over a plain suggestive one:

{
  type: 'LinearManhattanDisplay',
  encoding: {
    y: {
      axis: { title: '-log10 p' },
      rules: [{ value: 7.3, color: 'red', label: 'p = 5e-8' }, 5],
    },
  },
}

Three samples' coverage on one axis that still follows the data:

{
  type: 'LinearAlignmentsDisplay',
  coverage: { encoding: { y: { scale: { group: 'depth' } } } },
}

Config slots

A setting written to it names members one by one: a member left out stays as it is, and null resets one. Slot types (fileLocation, frozen, ...) are explained in the config slot types reference. Slots a base configuration contributes are listed here too, so this table is the whole surface.

SlotDescription
rules.value
number = 0		The rule's position on the axis, in the units the axis plots: a -log10(p) over a Manhattan plot, a depth over coverage.
rules.color
maybeColor		The line's color, and its label's. Unset draws every rule in the one color the chrome rules plots in, so a threshold that means something particular — genome-wide significance, a diploid depth — is one an author paints, on the plot where it means it.
rules.label
string = ''		Free text drawn at the rule's right-hand end. JBrowse assigns it no meaning: "2 copies" over a coverage plot is a claim only the author can make, since no ploidy can be assumed.
scale
YScale		type, domainMin, domainMax, zero, fenceQuantile, constant and group.
axis
YAxis		title and grid.
rules
list of ValueScaleRule entries		Horizontal reference lines, each { value, color, label } or a bare number. An autoscaled end widens to keep every rule on the axis; a pinned end that excludes one drops it.