genome_spy.SecondaryChromPosDef

class genome_spy.SecondaryChromPosDef(axis=Undefined, band=Undefined, chrom=Undefined, description=Undefined, domainInert=Undefined, offset=Undefined, pos=Undefined, title=Undefined, **kwds)View on GitHub

Bases: GenomeSpySchema

Generated wrapper for SecondaryChromPosDef.

Methods

axis([value, chromGrid, chromGridCap, ...])	Return a copy with a GenomeAxis axis.
band(value)	Return a copy with band updated.
chrom(value)	Return a copy with chrom updated.
copy(*[, deep])	Return a copy with optional keyword updates.
description(value)	Return a copy with description updated.
domainInert(value)	Return a copy with domainInert updated.
offset(value)	Return a copy with offset updated.
pos(value)	Return a copy with pos updated.
resolve_references()	Return this class schema with referenced properties merged in.
title(value)	Return a copy with title updated.
to_dict(*[, validate])	Serialize this schema wrapper to a JSON-compatible dictionary.
to_json(*[, validate])	Serialize this schema wrapper to formatted JSON.
validate(instance)	Validate an instance against this wrapper's schema.

axis(value=Undefined, /, *, chromGrid=Undefined, chromGridCap=Undefined, chromGridColor=Undefined, chromGridDash=Undefined, chromGridDashOffset=Undefined, chromGridFillEven=Undefined, chromGridFillOdd=Undefined, chromGridOpacity=Undefined, chromGridWidth=Undefined, chromLabelAlign=Undefined, chromLabelColor=Undefined, chromLabelFont=Undefined, chromLabelFontSize=Undefined, chromLabelFontStyle=Undefined, chromLabelFontWeight=Undefined, chromLabelPadding=Undefined, chromLabels=Undefined, chromTickColor=Undefined, chromTickDash=Undefined, chromTickDashOffset=Undefined, chromTickSize=Undefined, chromTickWidth=Undefined, chromTicks=Undefined, domain=Undefined, domainCap=Undefined, domainColor=Undefined, domainDash=Undefined, domainDashOffset=Undefined, domainWidth=Undefined, extraValues=Undefined, format=Undefined, grid=Undefined, gridCap=Undefined, gridColor=Undefined, gridDash=Undefined, gridDashOffset=Undefined, gridOpacity=Undefined, gridWidth=Undefined, labelAlign=Undefined, labelAngle=Undefined, labelBaseline=Undefined, labelColor=Undefined, labelFlush=Undefined, labelFlushOffset=Undefined, labelFont=Undefined, labelFontSize=Undefined, labelFontStyle=Undefined, labelFontWeight=Undefined, labelLimit=Undefined, labelOverlap=Undefined, labelPadding=Undefined, labelSeparation=Undefined, labelSqueeze=Undefined, labels=Undefined, maxExtent=Undefined, minExtent=Undefined, offset=Undefined, orient=Undefined, placement=Undefined, style=Undefined, tickCap=Undefined, tickColor=Undefined, tickCount=Undefined, tickDash=Undefined, tickDashOffset=Undefined, tickMinStep=Undefined, tickSize=Undefined, tickWidth=Undefined, ticks=Undefined, title=Undefined, titleColor=Undefined, titleFit=Undefined, titleFont=Undefined, titleFontSize=Undefined, titleFontStyle=Undefined, titleFontWeight=Undefined, titleOpacity=Undefined, titlePadding=Undefined, values=Undefined, zindex=Undefined)View on GitHub

Return a copy with a GenomeAxis axis.

Parameters:

• chromGrid (bool) – A boolean flag indicating if chromosome grid lines should be included as part of the axis. __Default value:__ false

• chromGridCap (Literal['butt', 'round', 'square']) – The stroke cap for the chromosome grid line’s ending style. One of "butt", "round" or "square". __Default value:__ "butt"

• chromGridColor (str | ExprRef | dict[str, Any]) – Color of grid lines. __Default value:__ lightgray

• chromGridDash (Sequence[float]) – An array of alternating [stroke, space] lengths for dashed chromosome grid mark lines.

• chromGridDashOffset (float) – The pixel offset at which to start drawing with the chromosome grid mark dash array.

• chromGridFillEven (str | ExprRef | dict[str, Any]) – Fill color of odd chromosomes. __Default value:__ (none)

• chromGridFillOdd (str | ExprRef | dict[str, Any]) – Fill color of odd chromosomes. __Default value:__ (none)

• chromGridOpacity (float) – The opacity of the chromosome grid lines. __Default value:__ 1

• chromGridWidth (float) – Width of the chromosome grid lines. __Default value:__ 1

• chromLabelAlign (Align_T) – Horizontal text alignment of chromosome name labels. __Default value:__ "left"

• chromLabelColor (str | ExprRef | dict[str, Any]) – Text color of chromosome name labels. __Default value:__ "black"

• chromLabelFont (str) – The font of chromosome name labels.

• chromLabelFontSize (float) – Font size of chromosome name labels, in pixels. __Default value:__ 13

• chromLabelFontStyle (FontStyle_T) – Font style of chromosome name labels. __Default value:__ "normal"

• chromLabelFontWeight (FontWeight_T) – Font weight of chromosome name labels. __Default value:__ "normal"

• chromLabelPadding (float) – The padding, in pixels, between chromosome boundary ticks and chromosome name labels. __Default value:__ 7

• chromLabels (bool) – A boolean flag indicating if chromosome name labels should be included as part of the genome axis. __Default value:__ true

• chromTickColor (str | ExprRef | dict[str, Any]) – The color of chromosome boundary ticks. __Default value:__ "#989898"

• chromTickDash (Sequence[float]) – An array of alternating [stroke, space] lengths for dashed chromosome boundary ticks. __Default value:__ [4, 2]

• chromTickDashOffset (float) – The pixel offset at which to start drawing with the chromosome tick dash array. __Default value:__ 1

• chromTickSize (float) – The size in pixels of chromosome boundary ticks. __Default value:__ 18

• chromTickWidth (float) – The width, in pixels, of chromosome boundary ticks. __Default value:__ 1

• chromTicks (bool) – A boolean flag indicating if chromosome boundary ticks should be included as part of the genome axis. __Default value:__ true

• domain (bool) – A boolean flag indicating if the domain (the axis baseline) should be included as part of the axis. __Default value:__ true

• domainCap (Literal['butt', 'round', 'square']) – The stroke cap for the domain line’s ending style. One of "butt", "round" or "square". __Default value:__ "butt"

• domainColor (str | ExprRef | dict[str, Any]) – Color of axis domain line. __Default value:__ "gray".

• domainDash (Sequence[float]) – An array of alternating [stroke, space] lengths for dashed domain lines.

• domainDashOffset (float) – The pixel offset at which to start drawing with the domain dash array.

• domainWidth (float) – Stroke width of axis domain line __Default value:__ 1

• extraValues (Sequence[float]) – Additional tick and label values to include alongside automatically generated ticks on continuous scales. Values outside the visible scale range are omitted and duplicates are removed. During automatic overlap removal, these labels are reduced against other explicitly specified labels but take precedence over automatically generated labels. This property is ignored on discrete scales and when values is set.

• format (str) – The format specifier pattern for axis labels. Must be a legal d3-format specifier.

• grid (bool) – A boolean flag indicating if grid lines should be included as part of the axis. __Default value:__ false

• gridCap (Literal['butt', 'round', 'square']) – The stroke cap for the grid line’s ending style. One of "butt", "round" or "square". __Default value:__ "butt"

• gridColor (str | ExprRef | dict[str, Any]) – Color of grid lines. __Default value:__ lightgray

• gridDash (Sequence[float]) – An array of alternating [stroke, space] lengths for dashed grid mark lines.

• gridDashOffset (float) – The pixel offset at which to start drawing with the grid mark dash array.

• gridOpacity (float) – The opacity of the grid lines. __Default value:__ 1

• gridWidth (float) – Width of the grid lines. __Default value:__ 1

• labelAlign (Align_T) – Horizontal text alignment of axis tick labels, overriding the default setting for the current axis orientation.

• labelAngle (float) – The rotation angle of the axis labels. __Default value:__ -90 for nominal and ordinal fields; 0 otherwise.

• labelBaseline (Baseline_T) – Vertical text baseline of axis tick labels, overriding the default setting for the current axis orientation. One of "alphabetic" (default), "top", "middle", "bottom".

• labelColor (str | ExprRef | dict[str, Any]) – The color of the tick label, can be in hex color code or regular color name.

• labelFlush (bool | float) – Indicates whether labels near the beginning or end of the axis should be aligned flush with the scale range. A number specifies the endpoint distance threshold in pixels. true uses a threshold of one pixel. Flushing is supported for quantitative, index, and locus axes. By default, it is enabled for non-zoomable x axes of these types. On a zoomable x axis with a configured bounded zoom extent, ticks matching the extent boundaries are flushed while they remain visible. Other zoomable ticks and y-axis ticks are not flushed by default. Flushing supports label angles that are multiples of 90 degrees. The automatic behavior is disabled at other angles.

• labelFlushOffset (float) – The number of pixels by which to move flush-adjusted labels outward from the axis range. __Default value:__ 0

• labelFont (str) – The font of the tick label.

• labelFontSize (float) – The font size of the label, in pixels.

• labelFontStyle (FontStyle_T) – Font style of the title.

• labelFontWeight (FontWeight_T) – Font weight of axis tick labels.

• labelLimit (float) – Maximum allowed pixel width of axis tick labels. __Default value:__ 180

• labelOverlap (bool | Literal['parity'] | Literal['greedy']) – The strategy for removing overlapping axis labels. true uses the "parity" strategy. "parity" removes every other label until the remaining labels no longer overlap. "greedy" keeps each label that does not overlap the previously retained label. false disables overlap removal. By default, overlap removal uses "parity" for linear-like continuous scales and "greedy" for logarithmic and symlog scales. It is disabled for discrete scales. Overlap removal supports label angles that are multiples of 90 degrees. The automatic behavior is disabled at other angles.

• labelPadding (float) – The padding, in pixels, between axis and text labels. __Default value:__ 2

• labelSeparation (float) – The minimum separation, in pixels, between retained axis labels. __Default value:__ 2

• labelSqueeze (bool) – Shrink each tick label uniformly to fit its band, accounting for label rotation. Supported only for band scales. Enables ranged text fitting and bypasses labelOverlap, including an explicitly configured strategy. Labels stay aligned with their bands at viewport edges. Very small labels fade out using the text mark’s normal fitting behavior. __Default value:__ false

• labels (bool) – A boolean flag indicating if labels should be included as part of the axis. __Default value:__ true.

• maxExtent (float) – The maximum extent in pixels that axis ticks and labels should use. This determines a maximum offset value for axis titles. __Default value:__ undefined.

• minExtent (float) – The minimum extent in pixels that axis ticks and labels should use. This determines a minimum offset value for axis titles. __Default value:__ 30 for y-axis; undefined for x-axis.

• offset (float) – The orthogonal offset in pixels by which to displace the axis from its position along the edge of the chart.

• orient (AxisOrient_T) – The orientation of the axis. One of "top", "bottom", "left" or "right". The orientation can be used to further specialize the axis type (e.g., a y axis oriented for the right edge of the chart). __Default value:__ "bottom" for x-axes and "left" for y-axes.

• placement (AxisPlacement_T) – Placement of the axis relative to the plotting area. Outside axes reserve layout space outside the plot. Inside axes are mirrored into the plot and do not reserve external layout space. __Default value:__ "outside".

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

• tickCap (Literal['butt', 'round', 'square']) – The stroke cap for the tick lines’ ending style. One of "butt", "round" or "square". __Default value:__ "butt"

• tickColor (str | ExprRef | dict[str, Any]) – The color of the axis’s tick. __Default value:__ "gray"

• tickCount (float | ExprRef | dict[str, Any]) – A desired number of ticks, for axes visualizing quantitative scales. The resulting number may be different so that values are “nice” (multiples of 2, 5, 10) and lie within the underlying scale’s range. An expression reference can use axisLength for the current length of the axis in pixels. For example, { "expr": "ceil(axisLength / 40)" } requests one tick per 40 pixels. __Default value:__ an expression based on axisLength

• tickDash (Sequence[float]) – An array of alternating [stroke, space] lengths for dashed tick mark lines.

• tickDashOffset (float) – The pixel offset at which to start drawing with the tick mark dash array.

• tickMinStep (float) – The minimum desired step between axis ticks, in terms of scale domain values. For example, a value of 1 indicates that ticks should not be less than 1 unit apart. If tickMinStep is specified, the tickCount value will be adjusted, if necessary, to enforce the minimum step value.

• tickSize (float) – The size in pixels of axis ticks. __Default value:__ 5

• tickWidth (float) – The width, in pixels, of ticks. __Default value:__ 1

• ticks (bool) – Boolean value that determines whether the axis should include ticks. __Default value:__ true

• title (str | None) – A title for the axis. By default, the title is derived from the encoding title, field, or expression. Set to null to remove it.

• titleColor (str | ExprRef | dict[str, Any]) – Color of the title, can be in hex color code or regular color name.

• titleFit (Literal['point', 'range']) – Fitting mode for the axis title. "point" anchors the title at the center of the axis without constraining its length. "range" constrains the title to the axis span using ranged text, allowing it to be squeezed to fit and kept visible inside scrollable viewports. __Default value:__ "point"

• titleFont (str) – Font of the title. (e.g., "Helvetica Neue").

• titleFontSize (float) – Font size of the title.

• titleFontStyle (FontStyle_T) – Font style of the title.

• titleFontWeight (FontWeight_T) – Font weight of the title. This can be either a string (e.g "bold", "normal") or a number (100, 200, 300, …, 900 where "normal" = 400 and "bold" = 700).

• titleOpacity (float) – Opacity of the axis title.

• titlePadding (float) – The padding, in pixels, between title and axis.

• values (Sequence[Any]) – Explicitly set the visible axis tick and label values. During automatic overlap removal, these labels are reduced against each other but take precedence over automatically generated labels.

• zindex (float) – Z-order of the axis relative to the view content. Values greater than 0 render after the view marks. Values less than or equal to 0 render before the marks. __Default value:__ 0, or 10 when the view content is clipped or scrollable.

band(value)View on GitHub

Return a copy with band updated.

chrom(value)View on GitHub

Return a copy with chrom updated.

description(value)View on GitHub

Return a copy with description updated.

domainInert(value)View on GitHub

Return a copy with domainInert updated.

offset(value)View on GitHub

Return a copy with offset updated.

pos(value)View on GitHub

Return a copy with pos updated.

title(value)View on GitHub

Return a copy with title updated.

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.