genome_spy.Shape

class genome_spy.Shape(value, /, *, band=Undefined, condition=Undefined, datum=Undefined, description=Undefined, domainInert=Undefined, expr=Undefined, field=Undefined, format=Undefined, resolutionChannel=Undefined, title=Undefined, type=Undefined, legend=Undefined, scale=Undefined)View on GitHub

Bases: Channel

Generated wrapper for the shape encoding channel.

Methods

band(value)

Return a channel with band updated.

condition(value)

Return a channel with condition updated.

datum(value)

Return a channel with datum updated.

description(value)

Return a channel with description updated.

domainInert(value)

Return a channel with domainInert updated.

expr(value)

Return a channel with expr updated.

field(value)

Return a channel with field updated.

format(value)

Return a channel with format updated.

legend([value, backgroundFill, ...])

Return a channel with a Legend legend.

resolutionChannel(value)

Return a channel with resolutionChannel updated.

scale([value, align, assembly, base, bins, ...])

Return a channel with a Scale scale.

sort([value, field, order])

Return a channel with a sort configuration.

title(value)

Return a channel with title updated.

to_dict()

Return the JSON-serializable channel definition.

type(value)

Return a channel with type updated.

value(value)

Return a channel with value updated.

Attributes

definition

encoding_name

band(value)View on GitHub

Return a channel with band updated.

condition(value)View on GitHub

Return a channel with condition updated.

datum(value)View on GitHub

Return a channel with datum updated.

description(value)View on GitHub

Return a channel with description updated.

domainInert(value)View on GitHub

Return a channel with domainInert updated.

expr(value)View on GitHub

Return a channel with expr updated.

field(value)View on GitHub

Return a channel with field updated.

format(value)View on GitHub

Return a channel with format updated.

resolutionChannel(value)View on GitHub

Return a channel with resolutionChannel updated.

title(value)View on GitHub

Return a channel with title updated.

type(value)View on GitHub

Return a channel with type updated.

value(value)View on GitHub

Return a channel with value updated.

sort(value=Undefined, /, *, field=Undefined, order=Undefined)View on GitHub

Return a channel with a sort configuration.

legend(value=Undefined, /, *, backgroundFill=Undefined, backgroundFillOpacity=Undefined, backgroundStroke=Undefined, backgroundStrokeOpacity=Undefined, backgroundStrokeWidth=Undefined, columns=Undefined, direction=Undefined, gradientLength=Undefined, gradientOpacity=Undefined, gradientStrokeColor=Undefined, gradientStrokeWidth=Undefined, gradientThickness=Undefined, labelLimit=Undefined, offset=Undefined, orient=Undefined, padding=Undefined, style=Undefined, symbolFillColor=Undefined, symbolOpacity=Undefined, symbolSize=Undefined, symbolStrokeColor=Undefined, symbolStrokeWidth=Undefined, symbolType=Undefined, tickCount=Undefined, title=Undefined, titleOrient=Undefined, values=Undefined)View on GitHub

Return a channel with a Legend legend.

Parameters:

  • backgroundFill (str) – Fill color of the legend background.

  • backgroundFillOpacity (float) – Opacity of the legend background fill.

  • backgroundStroke (str) – Stroke color of the legend background.

  • backgroundStrokeOpacity (float) – Opacity of the legend background stroke.

  • backgroundStrokeWidth (float) – Stroke width of the legend background border.

  • columns (float) – The number of columns in which to arrange symbol legend entries.

  • direction (LegendDirection_T) – The direction in which legend entries are laid out. This is independent of orient, which selects the legend region. __Default value:__ "vertical"

  • gradientLength (float) – Fixed length of the gradient ramp in pixels. This is the width of a horizontal ramp and the height of a vertical ramp. When omitted, the ramp fills available space when its direction is parallel to its legend region. Otherwise its natural length is 200 pixels.

  • gradientOpacity (float) – Opacity of the gradient ramp. __Default value:__ 1

  • gradientStrokeColor (str) – Stroke color of the gradient ramp border.

  • gradientStrokeWidth (float) – Stroke width of the gradient ramp border in pixels. __Default value:__ 0

  • gradientThickness (float) – Thickness of the gradient ramp in pixels. __Default value:__ 12

  • labelLimit (float) – Maximum label text width in pixels.

  • offset (float) – External gap in pixels between the legend and the plot edge.

  • orient (LegendOrient_T | ExprRef | dict[str, Any]) – The plot side or inside corner where the legend is placed. Side legends are placed outside the plot area. Corner legends are placed inside the plot area.

  • padding (float) – Internal padding in pixels around the legend content and background.

  • style (str | Sequence[str] | None) – Named style reference or references resolved from config.style. If an array is provided, later styles override earlier ones. Set to null to reset inherited legend styles.

  • symbolFillColor (str) – Symbol fill color. Overrides inherited fill styling, except when the legend encodes fill or uses fill to encode color.

  • symbolOpacity (float) – Symbol opacity. Overrides inherited mark and encoding opacity, except when the legend encodes opacity. Set to 1 to keep a category key opaque while selections dim the data marks.

  • symbolSize (float) – Symbol size in pixels squared. Overrides inherited styling, except when the legend encodes size.

  • symbolStrokeColor (str) – Symbol stroke color. Overrides inherited stroke styling, except when the legend encodes stroke or uses stroke to encode color.

  • symbolStrokeWidth (float) – Symbol stroke width in pixels. Overrides inherited styling, except when the legend encodes stroke width.

  • symbolType (str) – Symbol shape. Overrides inherited styling, except when the legend encodes shape.

  • tickCount (float) – Desired number of ticks for a quantitative gradient legend. Explicit values take precedence over this property. __Default value:__ 5

  • title (str | None) – Title text for the legend. If null, the title is removed.

  • titleOrient (LegendTitleOrient_T) – The side of the legend on which to place the title.

  • values (Sequence[str | float | bool]) – Explicit values to show in the legend. For discrete symbol legends, the values define an ordered subset of entries. For quantitative symbol and gradient legends, the values define the shown representative values or ticks.

scale(value=Undefined, /, *, align=Undefined, assembly=Undefined, base=Undefined, bins=Undefined, clamp=Undefined, constant=Undefined, domain=Undefined, domainMax=Undefined, domainMid=Undefined, domainMin=Undefined, domainTransition=Undefined, exponent=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, zero=Undefined, zoom=Undefined)View on GitHub

Return a channel with a Scale scale.

Parameters:

  • align (float) – The alignment of the steps within the scale range. This value must lie in the range [0,1]. A value of 0.5 indicates that the steps should be centered within the range. A value of 0 or 1 may be used to shift the bands to one side, say to position them adjacent to an axis. __Default value:__ 0.5

  • assembly (str | UrlGenomeDefinition | dict[str, Any] | InlineGenomeDefinition) – Genome assembly definition for locus scales. This can be: - A string reference to a named assembly (built-in or root-configured). - An inline anonymous assembly that defines either contigs or url. If undefined, the default genome from the genome store is used.

  • base (float) – The logarithm base of the log scale (default 10).

  • bins (Sequence[float]) – An array of bin boundaries over the scale domain. If provided, axes and legends will use the bin boundaries to inform the choice of tick marks and text labels.

  • clamp (bool) – If true, values that exceed the data domain are clamped to either the minimum or maximum range value __Default value:__ derived from the Vega-Lite scale config’s clamp (true by default).

  • constant (float) – A constant determining the slope of the symlog function around zero. Only used for symlog scales. __Default value:__ 1

  • domain (ScalarDomain_T | Sequence[ChromosomalLocus | dict[str, Any]] | SelectionDomainRef | dict[str, Any] | ViewportDomainRef | ExprRef | Sequence[float | str | bool | ExprRef | dict[str, Any]]) – Customized domain values. For quantitative fields, domain can take the form of a two-element array with minimum and maximum values. Vega-Lite piecewise scales can be created by providing a domain with more than two entries. For ordinal and nominal fields, domain can be an array that lists valid input values. The domain can also be defined by an expression reference that evaluates to the domain array. Array elements may also be expression references. All parameter names referenced by a scale, including selection-domain parameters, resolve from the view that owns the scale resolution. For a shared scale, declare controlling parameters on that owning composed view or an ancestor.

  • domainMax (float) – Sets the maximum value in the scale domain, overriding the domain property. This property is only intended for use with scales having continuous domains.

  • domainMid (float) – Inserts a single mid-point value into a two-element domain. The mid-point value must lie between the domain minimum and maximum values. This property can be useful for setting a midpoint for Vega-Lite diverging color scales. The domainMid property is only intended for use with scales supporting continuous, piecewise domains.

  • domainMin (float) – Sets the minimum value in the scale domain, overriding the domain property. This property is only intended for use with scales having continuous domains.

  • domainTransition (bool) – Controls whether domain updates are applied immediately or with a smooth transition. Set this to false to apply domain updates immediately. The default is true, except for domains that include ExprRef``s, which default to ``false unless overridden. __Default value:__ true, except false for ExprRef-driven domains.

  • exponent (float) – The exponent of the pow scale.

  • interpolate (ScaleInterpolate_T | ScaleInterpolateParams | ScaleInterpolateParamsKwds) – The interpolation method for range values. By default, a general interpolator for numbers, dates, strings and colors (in HCL space) is used. For color ranges, this property allows interpolation in alternative color spaces. Legal values include rgb, hsl, hsl-long, lab, hcl, hcl-long, cubehelix and cubehelix-long (‘-long’ variants use longer paths in polar coordinate spaces). If object-valued, this property accepts an object with a string-valued type property and an optional numeric gamma property applicable to rgb and cubehelix interpolators. For more, see the d3-interpolate documentation. __Default value:__ hcl

  • name (str) – The name of the scale. Names are optional but allow the scales to be referenced and found with the API.

  • nice (bool | float | dict[str, Any]) – Extending the domain so that it starts and ends on nice round values. This method typically modifies the scale’s domain, and may only extend the bounds to the nearest round value. Nicing is useful if the domain is computed from data and may be irregular. For example, for a domain of [0.201479…, 0.996679…], a nice domain might be [0.2, 1.0]. For quantitative scales such as linear, nice can be either a boolean flag or a number. If nice is a number, it will represent a desired tick count. This allows greater control over the step size used to extend the bounds, guaranteeing that the returned ticks will exactly cover the domain. __Default value:__ true for unbinned quantitative fields; false otherwise.

  • numberingOffset (float) – The offset added to data values when formatting tick labels on index and locus scales. This property does not transform data values. __Default value:__ 0

  • padding (float) – For Vega-Lite continuous scales, expands the scale domain to accommodate the specified number of pixels on each of the scale range. The scale range must represent pixels for this parameter to function as intended. Padding adjustment is performed prior to all other adjustments, including the effects of the zero, nice, domainMin, and domainMax properties. For Vega-Lite band scales, shortcut for setting paddingInner and paddingOuter to the same value. For Vega-Lite point scales, alias for paddingOuter. __Default value:__ For continuous scales, derived from the Vega-Lite scale config’s continuousPadding. For band and point scales, see paddingInner and paddingOuter. By default, Vega-Lite sets padding such that width/height = number of unique values * step.

  • paddingInner (float) – The inner padding (spacing) within each band step of band scales, as a fraction of the step size. This value must lie in the range [0,1]. For point scale, this property is invalid as point scales do not have internal band widths (only step sizes between bands). __Default value:__ derived from the Vega-Lite scale config’s bandPaddingInner.

  • paddingOuter (float) – The outer padding (spacing) at the ends of the range of band and point scales, as a fraction of the step size. This value must lie in the range [0,1]. __Default value:__ derived from the Vega-Lite scale config’s bandPaddingOuter for band scales and pointPadding for point scales. By default, Vega-Lite sets outer padding such that width/height = number of unique values * step.

  • range (Sequence[float | str | ExprRef | dict[str, Any]] | str) – The range of the scale. One of: - A string indicating a pre-defined named scale range from Vega-Lite (e.g., example, "symbol", or "diverging"). - For Vega-Lite continuous scales, two-element array indicating minimum and maximum values, or an array with more than two entries for specifying a Vega-Lite piecewise scale. Array elements may also be expression references, which use the parameter scope of the view that owns the scale resolution. - For Vega-Lite discrete and Vega-Lite discretizing scales, an array of desired output values. Array elements may also be expression references, which use the parameter scope of the view that owns the scale resolution. __Notes:__ 1) For color scales you can also specify a color scheme instead of range. 2) Any directly specified range for x and y channels will be ignored. Range can be customized via the view’s corresponding Vega-Lite size (width and height).

  • reverse (bool) – If true, reverses the order of the scale range. __Default value:__ false.

  • round (bool) – If true, rounds numeric output values to integers. This can be helpful for snapping to the pixel grid. __Default value:__ false.

  • scheme (str | SchemeParams | SchemeParamsKwds) – A string indicating a color Vega-Lite scheme name (e.g., "category10" or "blues") or a Vega-Lite scheme parameter object. Discrete color schemes may be used with Vega-Lite discrete or Vega-Lite discretizing scales. Continuous color schemes are intended for use with color scales. For the full list of supported schemes, please refer to the Vega Scheme reference.

  • type (ScaleType_T) – The type of scale. GenomeSpy follows the Vega-Lite scale model; the links below refer to the Vega-Lite documentation: 1) Continuous Scales – mapping continuous domains to continuous output ranges ("linear", "pow", "sqrt", "symlog", "log", "time", "utc"). 2) Discrete Scales – mapping discrete domains to discrete ("ordinal") or continuous ("band" and "point") output ranges. 3) Discretizing Scales – mapping continuous domains to discrete output ranges "bin-ordinal", "quantile", "quantize" and "threshold". GenomeSpy also provides index and locus scales for sequence and genomic coordinates. __Default value:__ please see the Vega-Lite scale type table.

  • zero (bool) – If true, ensures that a zero baseline value is included in the scale domain. __Default value:__ true for x and y channels if the quantitative field is not binned and no custom domain is provided; false otherwise. __Note:__ Log scales do not support zero.

  • zoom (bool | ZoomParams | ZoomParamsKwds) – If true and the scale is used on a positional channel, it can bee zoomed and translated interactively.

to_dict()View on GitHub

Return the JSON-serializable channel definition.