genome_spy.Scale

class genome_spy.Scale(align=Undefined, assembly=Undefined, base=Undefined, bins=Undefined, clamp=Undefined, constant=Undefined, domain=Undefined, domainMax=Undefined, domainMid=Undefined, domainMin=Undefined, domainTransition=Undefined, exponent=Undefined, gapPositions=Undefined, gapWidth=Undefined, interpolate=Undefined, name=Undefined, nice=Undefined, numberingOffset=Undefined, padding=Undefined, paddingInner=Undefined, paddingOuter=Undefined, range=Undefined, reverse=Undefined, round=Undefined, scheme=Undefined, type=Undefined, viewport=Undefined, zero=Undefined, zoom=Undefined, **kwds)View on GitHub

Bases: GenomeSpySchema

Generated wrapper for Scale.

Methods

align(value)	Return a copy with align updated.
assembly([value, contigs, url])	Return a copy with assembly updated.
base(value)	Return a copy with base updated.
bins(value)	Return a copy with bins updated.
clamp(value)	Return a copy with clamp updated.
constant(value)	Return a copy with constant updated.
copy(*[, deep])	Return a copy with optional keyword updates.
domain([value, encoding, expr, initial, ...])	Return a copy with domain updated.
domainMax(value)	Return a copy with domainMax updated.
domainMid(value)	Return a copy with domainMid updated.
domainMin(value)	Return a copy with domainMin updated.
domainTransition(value)	Return a copy with domainTransition updated.
exponent(value)	Return a copy with exponent updated.
gapPositions([value, expr])	Return a copy with a ExprRef gapPositions.
gapWidth([value, expr])	Return a copy with a ExprRef gapWidth.
interpolate([value, gamma, type])	Return a copy with interpolate updated.
name(value)	Return a copy with name updated.
nice([value, interval, step])	Return a copy with nice updated.
numberingOffset(value)	Return a copy with numberingOffset updated.
padding(value)	Return a copy with padding updated.
paddingInner(value)	Return a copy with paddingInner updated.
paddingOuter(value)	Return a copy with paddingOuter updated.
range(value)	Return a copy with range updated.
resolve_references()	Return this class schema with referenced properties merged in.
reverse(value)	Return a copy with reverse updated.
round(value)	Return a copy with round updated.
scheme([value, count, extent, name])	Return a copy with a SchemeParams scheme.
to_dict(*[, validate])	Serialize this schema wrapper to a JSON-compatible dictionary.
to_json(*[, validate])	Serialize this schema wrapper to formatted JSON.
type(value)	Return a copy with type updated.
validate(instance)	Validate an instance against this wrapper's schema.
viewport(value)	Return a copy with viewport updated.
zero(value)	Return a copy with zero updated.
zoom([value, extent])	Return a copy with a ZoomParams zoom.

align(value)View on GitHub

Return a copy with align updated.

assembly(value=Undefined, /, *, contigs=Undefined, url=Undefined)View on GitHub

Return a copy with assembly updated.

Parameters:

• contigs (Sequence[Contig | dict[str, Any]]) – An array of contigs/sequences in the genome assembly.

• url (str) – A URL to a chrom.sizes file, which is a tab-separated file with two columns: the sequence name and its size. You may want to strip alternative loci, haplotypes, and other non-canonical contigs from the file. Example: "https://genomespy.app/data/genomes/hg19/chrom.sizes"

base(value)View on GitHub

Return a copy with base updated.

bins(value)View on GitHub

Return a copy with bins updated.

clamp(value)View on GitHub

Return a copy with clamp updated.

constant(value)View on GitHub

Return a copy with constant updated.

domain(value=Undefined, /, *, encoding=Undefined, expr=Undefined, initial=Undefined, mode=Undefined, param=Undefined, source=Undefined)View on GitHub

Return a copy with domain updated.

Parameters:

• encoding (Literal['x', 'y']) – Selection interval channel to use. If omitted, GenomeSpy infers the channel from the scale channel when possible (e.g., x -> x, x2 -> x, y -> y, y2 -> y).

• expr (str) – The expression string.

• initial (ScalarDomain_T | Sequence[ChromosomalLocus | dict[str, Any]]) – Initial configured domain for the linked scale when the linked interval selection is empty. Only supported when the linked scale is zoomable. Clearing the linked interval selection resets the domain to the normal default/data-derived domain instead of restoring initial.

• mode (Literal['intersect', 'contain']) – Determines which positional values contribute to the domain. "intersect" includes intervals that overlap the viewport. "contain" requires both endpoints to be inside it, including its boundaries. Points use inclusive boundaries in either mode. Encoded values are tested before applying band placement or pixel offsets. __Default value:__ "intersect".

• param (str) – Name of an interval selection parameter that provides the domain. The name resolves from the view that owns the scale resolution.

• source (Literal['viewport']) – Derives the domain from data in the current positional viewport. The domain is updated shortly after navigation pauses. Normal data-derived domain options, such as zero and nice, still apply.

domainMax(value)View on GitHub

Return a copy with domainMax updated.

domainMid(value)View on GitHub

Return a copy with domainMid updated.

domainMin(value)View on GitHub

Return a copy with domainMin updated.

domainTransition(value)View on GitHub

Return a copy with domainTransition updated.

exponent(value)View on GitHub

Return a copy with exponent updated.

gapPositions(value=Undefined, /, *, expr=Undefined)View on GitHub

Return a copy with a ExprRef gapPositions.

Parameters:

expr (str) – The expression string.

gapWidth(value=Undefined, /, *, expr=Undefined)View on GitHub

Return a copy with a ExprRef gapWidth.

Parameters:

expr (str) – The expression string.

interpolate(value=Undefined, /, *, gamma=Undefined, type=Undefined)View on GitHub

Return a copy with interpolate updated.

Parameters:

• gamma (float) – Schema-defined gamma property.

• type (Literal['rgb', 'cubehelix', 'cubehelix-long']) – Schema-defined type property.

name(value)View on GitHub

Return a copy with name updated.

nice(value=Undefined, /, *, interval=Undefined, step=Undefined)View on GitHub

Return a copy with nice updated.

Parameters:

• interval (str) – Schema-defined interval property.

• step (float) – Schema-defined step property.

numberingOffset(value)View on GitHub

Return a copy with numberingOffset updated.

padding(value)View on GitHub

Return a copy with padding updated.

paddingInner(value)View on GitHub

Return a copy with paddingInner updated.

paddingOuter(value)View on GitHub

Return a copy with paddingOuter updated.

range(value)View on GitHub

Return a copy with range updated.

reverse(value)View on GitHub

Return a copy with reverse updated.

round(value)View on GitHub

Return a copy with round updated.

scheme(value=Undefined, /, *, count=Undefined, extent=Undefined, name=Undefined)View on GitHub

Return a copy with a SchemeParams scheme.

Parameters:

• count (float) – The number of colors to use in the scheme. This can be useful for scale types such as "quantize", which use the length of the scale range to determine the number of discrete bins for the scale domain.

• extent (Sequence[float]) – The extent of the color range to use. For example [0.2, 1] will rescale the color scheme such that color values in the range [0, 0.2) are excluded from the scheme.

• name (str) – A color scheme name for ordinal scales (e.g., "category10" or "blues"). For the full list of supported schemes, please refer to the Vega Scheme reference.

type(value)View on GitHub

Return a copy with type updated.

viewport(value)View on GitHub

Return a copy with viewport updated.

zero(value)View on GitHub

Return a copy with zero updated.

zoom(value=Undefined, /, *, extent=Undefined)View on GitHub

Return a copy with a ZoomParams zoom.

Parameters:

extent (ScalarDomain_T | Sequence[ChromosomalLocus | dict[str, Any]] | Literal['data'] | Literal['unbounded']) – The boundaries that limit zoom and pan interactions on continuous scales. Band and point scales use the full categorical domain as their bounds and accept only a boolean zoom property. A domain array sets explicit boundaries. "data" derives the boundaries from the data that contributes to the scale domain. For index and quantitative scales, "unbounded" allows zooming and panning without fixed boundaries. Locus scales do not support unbounded zoom. With an unbounded extent, the initial scale domain is used as the reference for the zoomLevel() expression helper and its channel-specific form, such as zoomLevel("x"). __Default value:__ The initial scale domain, except the whole genome for locus scales.

copy(*, deep=True, **kwds)View on GitHub

Return a copy with optional keyword updates.

classmethod resolve_references()View on GitHub

Return this class schema with referenced properties merged in.

to_dict(*, validate=True)View on GitHub

Serialize this schema wrapper to a JSON-compatible dictionary.

to_json(*, validate=True)View on GitHub

Serialize this schema wrapper to formatted JSON.

classmethod validate(instance)View on GitHub

Validate an instance against this wrapper’s schema.