Grammar Reference

This is the reference documentation for the Gosling grammar.

A Gosling visualization is created using a Gosling specification, which is a JSON object. The possible keys and values of the JSON object are determined by the Gosling grammar.

Specification Root

The root object a Gosling specification is a View with the following optional properties.

property	type	description
title	string	Title of the visualization
subtitle	number	Subtitle of the visualization, shown below the title
description	number	Description of the visualization, shown below the subtitle

Example:

{
  "title": "My First Gosling Visualization",
  "subtitle": "The first of many",
  "description": "This describes what you see",
  "tracks": [
    ...
  ]
}

View

There are two types of views: track-containing views, and view-containing views.

Track-containing view

A view which contains the "track" property defines the genomic location for all the tracks it contains.

info

Track-containing views can also take any Track property, which the tracks within it will inherit

property	type	description
tracks	(Track | Track-containing View)[]	The tracks or views that are contained within the view. The axes of these tracks and views will be synced together. Required.
alignment	string	One of "stack" or "overlay". If "overlay" is set, the tracks within the view will be overlaid on top of each other. If "stack" is set, the tracks will be placed next to each other. Default: "stack"

Example

This is an outline of a track-containing view.

{
  // Optional properties from Track that the tracks will inherit 
  "xDomain": {"chromosome": "chr1", "interval": [1, 3000500]},

  // Track-containing view specific properties 
  "alignment": "overlay", // How the tracks will be aligned
  "tracks": [
    ...
  ]
}

View-containing view

A view can also contain multiple views. The genomic axes of these sub-views will not be synced together.

property	type	description
views	View[]	Views to show within the view. If a view takes this property, the "tracks" property should not be set. In addition, the view cannot contain any Track properties.
arrangement	string	One of "parallel", "serial", "vertical", "horizontal"

Example

This is an outline of a Gosling specification containing multiple views.

{
  "arrangement": "horizontal", // can be "parallel", "serial", "vertical", "horizontal"
  "views": [
    ...
  ]
}

Optional properties

Regardless of whether a view contains tracks or views, a view can these additional properties:

property	type	description
zoomLimits	array
yOffset	number	Specify the y offset of views in the unit of pixels
yDomain	DomainInterval | DomainChrInterval | DomainChr	Specify the visible region of genomic y-axis
xOffset	number	Specify the x offset of views in the unit of pixels
xDomain	DomainInterval | DomainChrInterval | DomainChr	Specify the visible region of genomic x-axis
style	Style	Define the style of multive views. Will be overwritten by the style of children elements (e.g., view, track).
static	boolean	Whether to disable Zooming and Panning, Default: false.
spacing	number	The size of the gap (1) between tracks, (2) between views, and (3) of the origin of circular tracks. The effect of this property depends on where on the spec you specify the spacing. In a linear layout, this value is used in pixels, while in a circular layout, this value is used relative to the height of the tracks or views.
orientation	string	One of "horizontal", "vertical". Specify the orientation.
linkingId	string	Specify an ID for linking multiple views
layout	string	One of "linear", "circular". Specify the layout type of all tracks.
id	string	The ID of a view that is maintained for the use of JS API functions, e.g., positions of a view
centerRadius	number	Proportion of the radius of the center white space. Default: 0.3
assembly	string | array	A string that specifies the genome builds to use. Currently support "hg38", "hg19", "hg18", "hg17", "hg16", "mm10", "mm9", and "unknown". Note:: with "unknown" assembly, genomic axes do not show chrN: in labels.

Track

A track is a unit building block in Gosling which can be represented as a bar chart, a line chart, or an ideogram. The genomic range of multiple tracks can be synchronized when the tracks belong to the same View.

Track layout properties

These properties specify the layout and data to be used in the track.

property	type	description
data	JsonData | CsvData | BedData | BigWigData | MultivecData | BeddbData | VectorData | MatrixData | BamData | VcfData | GffData	Required.
zoomLimits	array
yOffset	number	Specify the y offset of views in the unit of pixels
yDomain	DomainInterval | DomainChrInterval | DomainChr	Specify the visible region of genomic y-axis
xOffset	number	Specify the x offset of views in the unit of pixels
xDomain	DomainInterval | DomainChrInterval | DomainChr	Specify the visible region of genomic x-axis
width	number	Specify the track width in pixels.
title	string	If defined, will show the textual label on the left-top corner of a track.
subtitle	string
style	Style	Define the style of multive views. Will be overwritten by the style of children elements (e.g., view, track).
static	boolean	Whether to disable Zooming and Panning, Default: false.
startAngle	number	Specify the start angle (in the range of [0, 360]) of circular tracks ({"layout": "circular"}).
spacing	number	The size of the gap (1) between tracks, (2) between views, and (3) of the origin of circular tracks. The effect of this property depends on where on the spec you specify the spacing. In a linear layout, this value is used in pixels, while in a circular layout, this value is used relative to the height of the tracks or views.
overlayOnPreviousTrack	boolean
outerRadius	number	Specify the outer radius of tracks when {"layout": "circular"}.
orientation	string	One of "horizontal", "vertical". Specify the orientation.
linkingId	string	Specify an ID for linking multiple views
layout	string	One of "linear", "circular". Specify the layout type of all tracks.
innerRadius	number	Specify the inner radius of tracks when ({"layout": "circular"}).
id	string	Assigned to uid in a HiGlass view config, used for API and caching.
height	number	Specify the track height in pixels.
endAngle	number	Specify the end angle (in the range of [0, 360]) of circular tracks ({"layout": "circular"}).
centerRadius	number	Proportion of the radius of the center white space. Default: 0.3
assembly	string | array	A string that specifies the genome builds to use. Currently support "hg38", "hg19", "hg18", "hg17", "hg16", "mm10", "mm9", and "unknown". Note:: with "unknown" assembly, genomic axes do not show chrN: in labels.

Track encoding properties

These properties specify how to associate data to visual elements.

property	type	description
mark	string	Required. One of "point", "line", "area", "bar", "rect", "text", "withinLink", "betweenLink", "rule", "triangleLeft", "triangleRight", "triangleBottom", "brush", "header".
ye	Y | ChannelValue
y1e	Y | ChannelValue
y1	Y | ChannelValue
y	Y | ChannelValue
xe	X | ChannelValue
x1e	X | ChannelValue
x1	X | ChannelValue
x	X | ChannelValue
visibility	VisibilityCondition[]
tooltip	Tooltip[]
text	Text | ChannelValue
strokeWidth	StrokeWidth | ChannelValue
stroke	Stroke | ChannelValue
stretch	boolean
size	Size | ChannelValue
row	Row | ChannelValue
overrideTemplate	boolean
opacity	Opacity | ChannelValue
flipY	boolean
experimental	experimental	Each object follows the format {"mouseEvents":"boolean | [MouseEventsDeep](reference#mouseeventsdeep)","performanceMode":"boolean"} ( )
displacement	Displacement	Each object follows the format {"padding":"number","type":"string"} ( One of "pile", "spread".)
dataTransform	DataTransform[]
color	Color | ChannelValue
baselineY	number

Example

This is a Gosling specification of a view containing a single track.

{
  "tracks": [
    {
      "layout": "linear",
      "width": 800,
      "height": 180,
      "data": {
        "url": "https://resgen.io/api/v1/tileset_info/?d=UvVPeLHuRDiYA3qwFlm7xQ",
        "type": "multivec",
        "row": "sample",
        "column": "position",
        "value": "peak",
        "categories": ["sample 1"],
        "binSize": 5
      },
      "mark": "bar",
      "x": {"field": "start", "type": "genomic"},
      "xe": {"field": "end", "type": "genomic"},
      "y": {"field": "peak", "type": "quantitative"}
    }
  ]
}

Track template property

A track can use a preset track template using this property.

property	type	description
template	string	The template to use with the track.

DummyTrack

A DummyTrack is a track that is used a placeholder in a Gosling visualization. Non-Gosling visualizations can be incorporated using it.

property	type	description
type	string	Required. Must be "dummy-track". Used to specify the dummy track
width	number	Specify the track width in pixels.
title	string	Text that gets shown on the DummyTrack
style	DummyTrackStyle	Defines how the track is styled
static	boolean	Must be "true". Whether to disable Zooming and Panning, Default: false.
orientation	string	One of "horizontal", "vertical". Specify the orientation.
layout	string	Must be "linear". Only linear layout are supported at this time
id	string	Assigned to uid in a HiGlass view config, used for API and caching.
height	number	Specify the track height in pixels.

Example

This is a Gosling specification containing a single DummyTrack.

{
  "tracks": [
      {
        "type": "dummy-track",
        "title": "Placeholder",
        "id": "my_track",
        "height": 200,
        "width": 300,
        "style": {"background": "#e6e6e6", "textFontSize": 8, "textFontWeight": "normal"}
      }
  ]
}

Visual Channel

Different visual channels are supported depending on the mark type.

mark type	supported visual channels
point	x, y, row, size, color, strokeWidth, opacity
line	x, y, row, color, strokeWidth
rect	x, xe, row, color, strokeWidth, opacity
bar	x, y, row, color, strokeWidth, opacity
area	x, y, row, color, strokeWidth
link	x, xe, x1, x1e, color, opacity
triangle	x, xe, row, size, color, opacity
text	x, xe, row, color, opacity

ChannelValue

property	type	description
value	number|string	Required. Assign a constant value for a visual channel.

X

X specifies a mark's position in the horizontal direction.

property	type	description
type	string	Must be "genomic". Specify the data type.
range	string[] | number[]	Values of the visual channel.
linkingId	string	Users need to assign a unique linkingId for linking views and Brushing and Linking
legend	boolean	Whether to display legend. Default: false
grid	boolean	Whether to display grid. Default: false
field	string	Name of the data field.
domain	DomainInterval | DomainChrInterval | DomainChr	Values of the data
axis	string	One of "none", "top", "bottom", "left", "right". Specify where should the axis be put
aggregate	string	One of "max", "min", "mean", "bin", "count". Specify how to aggregate data. Default: undefined

DomainInterval

property	type	description
interval	number[]	Required. Show a certain interval within entire chromosome

DomainChr

property	type	description
chromosome	string	Required.

DomainChrInterval

property	type	description
interval	number[]	Required.
chromosome	string	Required. If specified, only showing a certain interval in a chromosome.

Y

Y specifies a mark's position in the vertical direction.

property	type	description
zeroBaseline	boolean	Specify whether to use zero baseline. Default: true
type	string	One of "quantitative", "nominal", "genomic". Specify the data type.
range	string[] | number[]	Values of the visual channel.
linkingId	string	Users need to assign a unique linkingId for linking views and Brushing and Linking
legend	boolean	Whether to display legend. Default: false
grid	boolean	Whether to display grid. Default: false
flip	boolean	Whether to flip the y-axis. This is done by inverting the range property. Default: false
field	string	Name of the data field.
domain	string[] | number[] | DomainInterval | DomainChrInterval | DomainChr	Values of the data
baseline	string|number	Custom baseline of the y-axis. Default: 0
axis	string	One of "none", "top", "bottom", "left", "right". Specify where should the axis be put
aggregate	string	One of "max", "min", "mean", "bin", "count". Specify how to aggregate data. Default: undefined

Text

property	type	description
type	string	One of "quantitative", "nominal". Specify the data type
range	string[]	Ranges of visual channel values
field	string	Name of the data field
domain	string[]	Values of the data

Color

property	type	description
type	string	One of "quantitative", "nominal". Specify the data type
title	string	Title of the legend. Default: undefined
scaleOffset	number[]	Whether to use offset of the domain proportionally. This is bound to brushes on the color legend. Default: [0, 1]
scale	string	One of "linear", "log".
range	string[] | number[] | string	Determine the colors that should be bound to data value. Default properties are determined considering the field type.
legend	boolean	Whether to display legend. Default: false
field	string	Name of the data field
domain	string[] | number[]	Values of the data

Size

property	type	description
type	string	One of "quantitative", "nominal". Specify the data type
range	string[] | number[]	Ranges of visual channel values
field	string	Name of the data field
domain	string[] | number[]	Values of the data

Row

Row is used with to stratify a visualization with categorical values.

property	type	description
type	string	Must be "nominal". Specify the data type
range	string[] | number[]	Determine the start and end position of rendering area of this track along vertical axis. Default: [0, height]
padding	number	Determines the size of inner white spaces on the top and bottom of individiual rows. Default: 0
legend	boolean	Whether to display legend. Default: false
grid	boolean	Whether to display grid. Default: false
field	string	Name of the data field
domain	string[] | number[]	Values of the data
clip	boolean	Clip row when the actual y value exceeds the max value of the y scale. Used only for bar marks at the moment. Default: true

Opacity

property	type	description
type	string	One of "quantitative", "nominal". Specify the data type
range	string[] | number[]	Ranges of visual channel values
field	string	Name of the data field
domain	string[] | number[]	Values of the data

Stroke

property	type	description
type	string	One of "quantitative", "nominal". Specify the data type
title	string	Title of the legend. Default: undefined
scaleOffset	number[]	Whether to use offset of the domain proportionally. This is bound to brushes on the color legend. Default: [0, 1]
range	string[] | number[] | string	Ranges of visual channel values
legend	boolean	Whether to display legend. Default: false
field	string	Name of the data field
domain	string[] | number[]	Values of the data

StrokeWidth

property	type	description
type	string	One of "quantitative", "nominal". Specify the data type
range	string[] | number[]	Ranges of visual channel values
field	string	Name of the data field
domain	string[] | number[]	Values of the data

VisibilityCondition

These are for semantic zoom.

SizeVisibilityCondition

property	type	description
threshold	number | string	Required. Specify the threshold as one of: A number representing a fixed threshold in the unit of pixels; "|xe-x|", using the distance between xe and x as threshold
target	string	Required. One of "track", "mark". Target specifies the object that you want to compare with the threshold.
operation	string	Required. One of "less-than", "lt", "LT", "greater-than", "gt", "GT", "less-than-or-equal-to", "ltet", "LTET", "greater-than-or-equal-to", "gtet", "GTET". A string that specifies the logical operation to conduct between threshold and the measure of target. Support greater than : "greater-than", "gt", "GT" less than : "less-than", "lt", "LT" greater than or equal to : "greater-than-or-equal-to", "gtet", "GTET" less than or equal to : "less-than-or-equal-to", "ltet", "LTET"
measure	string	Required. One of "width", "height". Specify which aspect of the target will be compared to the threshold.
transitionPadding	number	Specify the buffer size (in pixel) of width or height for smooth transition. Default: 0
conditionPadding	number	Specify the buffer size (in pixel) of width or height when calculating the visibility. Default: 0

ZoomLevelVisibilityCondition

property	type	description
threshold	number	Required. Set a threshold in the unit of base pairs (bp)
target	string	Required. One of "track", "mark". Target specifies the object that you want to compare with the threshold.
operation	string	Required. One of "less-than", "lt", "LT", "greater-than", "gt", "GT", "less-than-or-equal-to", "ltet", "LTET", "greater-than-or-equal-to", "gtet", "GTET". A string that specifies the logical operation to conduct between threshold and the measure of target. Support greater than : "greater-than", "gt", "GT" less than : "less-than", "lt", "LT" greater than or equal to : "greater-than-or-equal-to", "gtet", "GTET" less than or equal to : "less-than-or-equal-to", "ltet", "LTET"
measure	string	Required. Must be "zoomLevel". Specify which aspect of the target will be compared to the threshold.
transitionPadding	number	Specify the buffer size (in pixel) of width or height for smooth transition. Default: 0
conditionPadding	number	Specify the buffer size (in pixel) of width or height when calculating the visibility. Default: 0

Tooltip

property	type	description
type	string	Required. One of "genomic", "nominal", "quantitative". Type of the data field.
field	string	Required. Specifiy a data field whose value will show in the tooltip.
format	string	format of the data value.
alt	string	Name of the data field for showing in the tooltip. Will use the field name if not specified.

Style

A View and Track have a style property which can be set to an object with the following properties.

property	type	description
withinLinkVerticalLines	boolean	Whether to show vertical lines that connect to the baseline (axis) when y and ye are both used. Default: false
textStrokeWidth	number	Specify the stroke width of text marks. Can also be specified using the strokeWidth channel option of text marks.
textStroke	string	Specify the stroke of text marks. Can also be specified using the stroke channel option of text marks.
textFontWeight	string	One of "bold", "normal". Specify the font weight of text marks.
textFontSize	number	Specify the font size of text marks. Can also be specified using the size channel option of text marks.
textAnchor	string	One of "start", "middle", "end". Specify the alignment of text marks to a given point.
select	EventStyle	Customize visual effects of rangeSelect events on marks .
outlineWidth	number
outline	string
mouseOver	EventStyle	Customize visual effects of mouseOver events on marks.
matrixExtent	string	One of "full", "upper-right", "lower-left". Determine to show only one side of the diagonal in a HiGlass matrix. Default: "full"
linkStyle	string	One of "elliptical", "circular", "straight". The style of withinLink and betweenLink marks. Default: 'circular' 'elliptical' will be used as a default option.
linkMinHeight	number	The minimum height of withinLink and betweenLink marks. Unit is a percentagle. Default: 0.5
linkConnectionType	string	One of "straight", "curve", "corner". Specify the connetion type of betweenLink marks. Default: "corner"
linePattern	linePattern	Each object follows the format {"size":"number","type":"string"} ( One of "triangleLeft", "triangleRight".) Specify the pattern of dashes and gaps for rule marks.
legendTitle	string	If defined, show legend title on the top or left
inlineLegend	boolean	Specify whether to show legend in a single horizontal line?
enableSmoothPath	boolean	Whether to enable smooth paths when drawing curves. Default: false
dy	number	Offset the position of marks in y direction. This property is currently only supported for text marks.
dx	number	Offset the position of marks in x direction. This property is currently only supported for text marks
dashed	number[]	Specify the pattern of dashes and gaps for rule marks.
curve	string	One of "top", "bottom", "left", "right". Specify the curve of rule marks.
brush	brush	Customize the style of the brush mark in the rangeSelect mouse event.
backgroundOpacity	number
background	string
align	string	One of "left", "right". Specify the alignment of marks. This property is currently only supported for triangle marks.

linePattern

property	type	description
type	string	Required. One of "triangleLeft", "triangleRight".
size	number	Required.

EventStyle

property	type	description
strokeWidth	number	stroke width of the marks when mouse events are triggered
strokeOpacity	number
stroke	string	stroke color of the marks when mouse events are triggered
opacity	number	opacity of the marks when mouse events are triggered
color	string	color of the marks when mouse events are triggered
arrange	string	One of "behind", "front". Show event effects behind or in front of marks.

Brush

property	type	description
strokeWidth	number	stroke width of the marks when mouse events are triggered
strokeOpacity	number
stroke	string	stroke color of the marks when mouse events are triggered
opacity	number	opacity of the marks when mouse events are triggered
color	string	color of the marks when mouse events are triggered

DummyTrackStyle

A DummyTrack can take an style object with the following properties:

property	type	description
textStrokeWidth	number	Specify the stroke width of the title.
textStroke	string	Specify the stroke color of title.
textFontWeight	string	One of "bold", "normal". Specify the font weight of the title.
textFontSize	number	Specify the font size of the title
outline	string	Color of the outline of the track
background	string	Background color of the track

Data

JsonData

property	type	description
values	Datum[]	Required. Values in the form of JSON.
type	string	Required. Must be "json". Define data type.
sampleLength	number	Specify the number of rows loaded from the URL. Default: 1000
genomicFieldsToConvert	object[]	Experimental Proerty. Each object follows the format {"chromosomeField":"string","genomicFields":"string[]"} ( )
genomicFields	string[]	Specify the name of genomic data fields.
chromosomeField	string	Specify the name of chromosome data fields.

Datum

property	type	description
stringKey	number|string	Values in the form of JSON.

CsvData

property	type	description
url	string	Required. Specify the URL address of the data file.
type	string	Required. Must be "csv".
separator	string	Specify file separator, Default: ','
sampleLength	number	Specify the number of rows loaded from the URL. Default: 1000
longToWideId	string	Experimental Proerty.
headerNames	string[]	Specify the names of data fields if a CSV file does not contain a header.
genomicFieldsToConvert	object[]	Experimental Proerty. Each object follows the format {"chromosomeField":"string","genomicFields":"string[]"} ( )
genomicFields	string[]	Specify the name of genomic data fields.
chromosomePrefix	string	Specify the chromosome prefix if chromosomes are denoted using a prefix besides "chr" or a number
chromosomeField	string	Specify the name of chromosome data fields.

BedData

property	type	description
url	string	Required. Specify the URL address of the data file.
type	string	Required. Must be "bed".
indexUrl	string	Required. Specify the URL address of the data file index.
sampleLength	number	Specify the number of rows loaded from the URL. Default: 1000
customFields	string[]	An array of strings, where each string is the name of a non-standard field in the BED file. If there are n custom fields, we assume that the last n columns of the BED file correspond to the custom fields.

BigWigData

property	type	description
url	string	Required. Specify the URL address of the data file.
type	string	Required. Must be "bigwig".
value	string	Assign a field name of quantitative values. Default: "value"
start	string	Assign a field name of the start position of genomic intervals. Default: "start"
end	string	Assign a field name of the end position of genomic intervals. Default: "end"
column	string	Assign a field name of the middle position of genomic intervals. Default: "position"
binSize	number	Binning the genomic interval in tiles (unit size: 256).
aggregation	string	One of "mean", "sum". Determine aggregation function to apply within bins. Default: "mean"

MultivecData

property	type	description
url	string	Required. Specify the URL address of the data file.
type	string	Required. Must be "multivec".
value	string	Assign a field name of quantitative values. Default: "value"
start	string	Assign a field name of the start position of genomic intervals. Default: "start"
row	string	Assign a field name of samples. Default: "category"
end	string	Assign a field name of the end position of genomic intervals. Default: "end"
column	string	Assign a field name of the middle position of genomic intervals. Default: "position"
categories	string[]	assign names of individual samples.
binSize	number	Binning the genomic interval in tiles (unit size: 256).
aggregation	string	One of "mean", "sum". Determine aggregation function to apply within bins. Default: "mean"

BeddbData

property	type	description
url	string	Required. Specify the URL address of the data file.
type	string	Required. Must be "beddb".
genomicFields	object[]	Required. Each object follows the format {"index":"number","name":"string"} ( ) Specify the name of genomic data fields.
valueFields	object[]	Each object follows the format {"index":"number","name":"string","type":"string"} ( One of "nominal", "quantitative".) Specify the column indexes, field names, and field types.
exonIntervalFields	[object, object]	Experimental Proerty.

VectorData

property	type	description
url	string	Required. Specify the URL address of the data file.
type	string	Required. Must be "vector".
value	string	Assign a field name of quantitative values. Default: "value"
start	string	Assign a field name of the start position of genomic intervals. Default: "start"
end	string	Assign a field name of the end position of genomic intervals. Default: "end"
column	string	Assign a field name of the middle position of genomic intervals. Default: "position"
binSize	number	Binning the genomic interval in tiles (unit size: 256).
aggregation	string	One of "mean", "sum". Determine aggregation function to apply within bins. Default: "mean"

MatrixData

property	type	description
url	string	Required. URL link to the matrix data file
type	string	Required. Must be "matrix".
value	string	The name of the value field. Default: value
row	string	The name of the first genomic field. Default: y
column	string	The name of the first genomic field. Default: x
binSize	number	Determine the number of nearby cells to aggregate. Default: 1

BamData

property	type	description
url	string	Required. URL link to the BAM data file
type	string	Required. Must be "bam".
indexUrl	string	Required. URL link to the index file of the BAM file
maxInsertSize	number	Determines the threshold of insert sizes for determining the structural variants. Default: 5000
loadMates	boolean	Load mates that are located in the same chromosome. Default: false
junctionMinCoverage	number	Determine the threshold of coverage when extracting exon-to-exon junctions. Default: 1
extractJunction	boolean	Determine whether to extract exon-to-exon junctions. Default: false

VcfData

property	type	description
url	string	Required. URL link to the VCF file
type	string	Required. Must be "vcf".
indexUrl	string	Required. URL link to the tabix index file
sampleLength	number	The maximum number of rows to be loaded from the URL. Default: 1000

GffData

property	type	description
url	string	Required. URL link to the GFF file
type	string	Required. Must be "gff".
indexUrl	string	Required. URL link to the tabix index file
sampleLength	number	The maximum number of samples to be shown on the track. Samples are uniformly randomly selected so that this threshold is not exceeded. Default: 1000
attributesToFields	object[]	Each object follows the format {"attribute":"string","defaultValue":"string"} ( ) Specifies which attributes to include as a fields. GFF files have an "attributes" column which contains a list of attributes which are each tag-value pairs (tag=value). This option allows for specific attributes to be accessible as a field. For example, if you have an attribute called "gene_name" and you want label features on your track using those values, you can use this option so that you can use "field": "gene_name" in the schema. If there is a single value corresponding to the tag, Gosling will parse that value as a string. If there are multiple values corresponding to a tag, Gosling will parse it as a comma-separated list string. If a feature does not have a particular attribute, then the attribute value will be set to the defaultValue.

DataTransform

OneOfFilter

property	type	description
type	string	Required. Must be "filter".
oneOf	array	Required. Check whether the value is an element in the provided list.
field	string	Required. A filter is applied based on the values of the specified data field
not	boolean	when {"not": true}, apply a NOT logical operation to the filter. Default: false

IncludeFilter

property	type	description
type	string	Required. Must be "filter".
include	string	Required. Check whether the value includes a substring.
field	string	Required. A filter is applied based on the values of the specified data field
not	boolean	when {"not": true}, apply a NOT logical operation to the filter. Default: false

StrConcatTransform

property	type	description
type	string	Required. Must be "concat".
separator	string	Required.
newField	string	Required.
fields	string[]	Required.

StrReplaceTransform

property	type	description
type	string	Required. Must be "replace".
replace	object[]	Required. Each object follows the format {"from":"string","to":"string"} ( )
newField	string	Required.
field	string	Required.

LogTransform

property	type	description
type	string	Required. Must be "log".
field	string	Required.
newField	string	If specified, store transformed values in a new field.
base	number | string	If not specified, 10 is used.

DisplaceTransform

property	type	description
type	string	Required. Must be "displace".
newField	string	Required.
method	string	Required. One of "pile", "spread". A string that specifies the type of displacement.
boundingBox	boundingBox	Required.
maxRows	number	Specify maximum rows to be generated (default has no limit).

boundingBox

property	type	description
startField	string	Required. The name of a quantitative field that represents the start position.
endField	string	Required. The name of a quantitative field that represents the end position.
padding	number	The padding around visual lements. Either px or bp
isPaddingBP	boolean	Whether to consider padding as the bp length.
groupField	string	The name of a nominal field to group rows by in prior to piling-up.

ExonSplitTransform

property	type	description
type	string	Required. Must be "exonSplit".
separator	string	Required.
flag	flag	Required. Each object follows the format {"field":"string","value":"number|string"} ( )
fields	object[]	Required. Each object follows the format {"chrField":"string","field":"string","newField":"string","type":"string"} ( One of "genomic", "nominal", "quantitative".)

GenomicLengthTransform

property	type	description
type	string	Required. Must be "genomicLength".
startField	string	Required.
newField	string	Required.
endField	string	Required.

SvTypeTransform

property	type	description
type	string	Required. Must be "svType".
secondBp	secondBp	Required. Based on the BEDPE, infer SV types. SV types are specified as one of the following strings: DUP, TRA, DEL, t2tINV, h2hINV.
newField	string	Required.
firstBp	firstBp	Required. Based on the BEDPE, infer SV types. SV types are specified as one of the following strings: DUP, TRA, DEL, t2tINV, h2hINV.

firstBp

property	type	description
strandField	string	Required.
posField	string	Required.
chrField	string	Required.

secondBp

property	type	description
strandField	string	Required.
posField	string	Required.
chrField	string	Required.

CoverageTransform

property	type	description
type	string	Required. Must be "coverage".
startField	string	Required.
endField	string	Required.
newField	string
groupField	string	The name of a nominal field to group rows by in prior to piling-up

JsonParseTransform

property	type	description
type	string	Required. Must be "subjson".
genomicLengthField	string	Required. Length of genomic interval.
genomicField	string	Required. Relative genomic position to parse.
field	string	Required. The field that contains the JSON object array.
baseGenomicField	string	Required. Base genomic position when parsing relative position.