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gosling.schema.json
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gosling.schema.json
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{
"$ref": "#/definitions/GoslingSpec",
"$schema": "http://json-schema.org/draft-07/schema#",
"definitions": {
"Aggregate": {
"enum": [
"max",
"min",
"mean",
"bin",
"count"
],
"type": "string"
},
"Assembly": {
"enum": [
"hg38",
"hg19",
"hg18",
"hg17",
"hg16",
"mm10",
"mm9",
"unknown"
],
"type": "string"
},
"AxisPosition": {
"enum": [
"none",
"top",
"bottom",
"left",
"right"
],
"type": "string"
},
"BAMData": {
"additionalProperties": false,
"description": "Binary Alignment Map (BAM) is the comprehensive raw data of genome sequencing; it consists of the lossless, compressed binary representation of the Sequence Alignment Map-files.",
"properties": {
"indexUrl": {
"description": "URL link to the index file of the BAM file",
"type": "string"
},
"loadMates": {
"type": "boolean"
},
"maxInsertSize": {
"type": "number"
},
"type": {
"const": "bam",
"type": "string"
},
"url": {
"description": "URL link to the BAM data file",
"type": "string"
}
},
"required": [
"type",
"url",
"indexUrl"
],
"type": "object"
},
"BEDDBData": {
"additionalProperties": false,
"description": "Regular BED or similar files can be pre-aggregated for the scalable data exploration. Find our more about this format at [HiGlass Docs](https://docs.higlass.io/data_preparation.html#bed-files).",
"properties": {
"exonIntervalFields": {
"description": "experimental",
"items": [
{
"additionalProperties": false,
"properties": {
"index": {
"type": "number"
},
"name": {
"type": "string"
}
},
"required": [
"index",
"name"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"index": {
"type": "number"
},
"name": {
"type": "string"
}
},
"required": [
"index",
"name"
],
"type": "object"
}
],
"maxItems": 2,
"minItems": 2,
"type": "array"
},
"genomicFields": {
"description": "Specify the name of genomic data fields.",
"items": {
"additionalProperties": false,
"properties": {
"index": {
"type": "number"
},
"name": {
"type": "string"
}
},
"required": [
"index",
"name"
],
"type": "object"
},
"type": "array"
},
"type": {
"const": "beddb",
"type": "string"
},
"url": {
"description": "Specify the URL address of the data file.",
"type": "string"
},
"valueFields": {
"description": "Specify the column indexes, field names, and field types.",
"items": {
"additionalProperties": false,
"properties": {
"index": {
"type": "number"
},
"name": {
"type": "string"
},
"type": {
"enum": [
"nominal",
"quantitative"
],
"type": "string"
}
},
"required": [
"index",
"name",
"type"
],
"type": "object"
},
"type": "array"
}
},
"required": [
"type",
"url",
"genomicFields"
],
"type": "object"
},
"BIGWIGData": {
"additionalProperties": false,
"properties": {
"binSize": {
"description": "Binning the genomic interval in tiles (unit size: 256).",
"type": "number"
},
"column": {
"description": "Assign a field name of the middle position of genomic intervals.",
"type": "string"
},
"end": {
"description": "Assign a field name of the end position of genomic intervals.",
"type": "string"
},
"start": {
"description": "Assign a field name of the start position of genomic intervals.",
"type": "string"
},
"type": {
"const": "bigwig",
"type": "string"
},
"url": {
"description": "Specify the URL address of the data file.",
"type": "string"
},
"value": {
"description": "Assign a field name of quantitative values.",
"type": "string"
}
},
"required": [
"type",
"url",
"column",
"value"
],
"type": "object"
},
"CSVData": {
"additionalProperties": false,
"description": "Any small enough tabular data files, such as tsv, csv, BED, BEDPE, and GFF, can be loaded using \"csv\" data specification.",
"properties": {
"chromosomeField": {
"description": "Specify the name of chromosome data fields.",
"type": "string"
},
"chromosomePrefix": {
"description": "experimental",
"type": "string"
},
"genomicFields": {
"description": "Specify the name of genomic data fields.",
"items": {
"type": "string"
},
"type": "array"
},
"genomicFieldsToConvert": {
"description": "experimental",
"items": {
"additionalProperties": false,
"properties": {
"chromosomeField": {
"type": "string"
},
"genomicFields": {
"items": {
"type": "string"
},
"type": "array"
}
},
"required": [
"chromosomeField",
"genomicFields"
],
"type": "object"
},
"type": "array"
},
"headerNames": {
"description": "Specify the names of data fields if a CSV file is headerless.",
"items": {
"type": "string"
},
"type": "array"
},
"longToWideId": {
"description": "experimental",
"type": "string"
},
"quantitativeFields": {
"description": "Specify the name of quantitative data fields.",
"items": {
"type": "string"
},
"type": "array"
},
"sampleLength": {
"description": "Specify the number of rows loaded from the URL.\n\n__Default:__ `1000`",
"type": "number"
},
"separator": {
"description": "Specify file separator, __Default:__ ','",
"type": "string"
},
"type": {
"const": "csv",
"type": "string"
},
"url": {
"description": "Specify the URL address of the data file.",
"type": "string"
}
},
"required": [
"type",
"url"
],
"type": "object"
},
"Channel": {
"anyOf": [
{
"$ref": "#/definitions/ChannelDeep"
},
{
"$ref": "#/definitions/ChannelValue"
}
]
},
"ChannelBind": {
"additionalProperties": false,
"properties": {
"aggregate": {
"$ref": "#/definitions/Aggregate"
},
"bind": {
"$ref": "#/definitions/ChannelType"
}
},
"required": [
"bind"
],
"type": "object"
},
"ChannelDeep": {
"anyOf": [
{
"$ref": "#/definitions/X"
},
{
"$ref": "#/definitions/Y"
},
{
"$ref": "#/definitions/Row"
},
{
"$ref": "#/definitions/Color"
},
{
"$ref": "#/definitions/Size"
},
{
"$ref": "#/definitions/Stroke"
},
{
"$ref": "#/definitions/StrokeWidth"
},
{
"$ref": "#/definitions/Opacity"
},
{
"$ref": "#/definitions/Text"
}
]
},
"ChannelType": {
"type": "string"
},
"ChannelValue": {
"additionalProperties": false,
"properties": {
"value": {
"type": [
"number",
"string"
]
}
},
"required": [
"value"
],
"type": "object"
},
"Chromosome": {
"enum": [
"1",
"2",
"3",
"4",
"5",
"6",
"7",
"8",
"9",
"10",
"11",
"12",
"13",
"14",
"15",
"16",
"17",
"18",
"19",
"20",
"21",
"22",
"X",
"Y",
"M",
"chr1",
"chr2",
"chr3",
"chr4",
"chr5",
"chr6",
"chr7",
"chr8",
"chr9",
"chr10",
"chr11",
"chr12",
"chr13",
"chr14",
"chr15",
"chr16",
"chr17",
"chr18",
"chr19",
"chr20",
"chr21",
"chr22",
"chrX",
"chrY",
"chrM"
],
"type": "string"
},
"Color": {
"additionalProperties": false,
"properties": {
"baseline": {
"type": [
"string",
"number"
]
},
"domain": {
"$ref": "#/definitions/ValueExtent"
},
"field": {
"type": "string"
},
"legend": {
"type": "boolean"
},
"range": {
"$ref": "#/definitions/Range"
},
"type": {
"enum": [
"quantitative",
"nominal"
],
"type": "string"
},
"zeroBaseline": {
"type": "boolean"
}
},
"type": "object"
},
"Column": {
"additionalProperties": false,
"properties": {
"domain": {
"$ref": "#/definitions/ValueExtent"
},
"field": {
"type": "string"
},
"range": {
"$ref": "#/definitions/ValueExtent"
},
"type": {
"const": "nominal",
"type": "string"
}
},
"type": "object"
},
"CombineMatesTransform": {
"additionalProperties": false,
"description": "By looking up ids, combine mates (a pair of reads) into a single row, performing long-to-wide operation. Result data have `{field}` and `{field}_2` names.",
"properties": {
"idField": {
"type": "string"
},
"isLongField": {
"type": "string"
},
"maintainDuplicates": {
"type": "boolean"
},
"maxInsertSize": {
"type": "number"
},
"type": {
"const": "combineMates",
"type": "string"
}
},
"required": [
"type",
"idField"
],
"type": "object"
},
"CoverageTransform": {
"additionalProperties": false,
"description": "Aggregate rows and calculate coverage",
"properties": {
"endField": {
"type": "string"
},
"groupField": {
"description": "The name of a nominal field to group rows by in prior to piling-up",
"type": "string"
},
"newField": {
"type": "string"
},
"startField": {
"type": "string"
},
"type": {
"const": "coverage",
"type": "string"
}
},
"required": [
"type",
"startField",
"endField"
],
"type": "object"
},
"DataDeep": {
"anyOf": [
{
"$ref": "#/definitions/JSONData"
},
{
"$ref": "#/definitions/CSVData"
},
{
"$ref": "#/definitions/BIGWIGData"
},
{
"$ref": "#/definitions/MultivecData"
},
{
"$ref": "#/definitions/BEDDBData"
},
{
"$ref": "#/definitions/VectorData"
},
{
"$ref": "#/definitions/MatrixData"
},
{
"$ref": "#/definitions/BAMData"
}
]
},
"DataTrack": {
"additionalProperties": false,
"description": "Partial specification of `BasicSingleTrack` to use default visual encoding predefined by data type.",
"properties": {
"_invalidTrack": {
"description": "internal",
"type": "boolean"
},
"_renderingId": {
"description": "internal",
"type": "string"
},
"assembly": {
"$ref": "#/definitions/Assembly",
"description": "A string that specifies the genome builds to use. Currently support `\"hg38\"`, `\"hg19\"`, `\"hg18\"`, `\"hg17\"`, `\"hg16\"`, `\"mm10\"`, `\"mm9\"`, and `\"unknown\"`.\n\n__Note:__: with `\"unknown\"` assembly, genomic axes do not show chrN: in labels."
},
"centerRadius": {
"description": "Proportion of the radius of the center white space.\n\n__Default:__ 0.3",
"type": "number"
},
"data": {
"$ref": "#/definitions/DataDeep"
},
"endAngle": {
"description": "Specify the end angle (in the range of [0, 360]) of circular tracks (`{\"layout\": \"circular\"}`).",
"type": "number"
},
"height": {
"description": "Specify the track height in pixels.",
"type": "number"
},
"id": {
"type": "string"
},
"innerRadius": {
"description": "Specify the inner radius of tracks when (`{\"layout\": \"circular\"}`).",
"type": "number"
},
"layout": {
"$ref": "#/definitions/Layout",
"description": "Specify the layout type of all tracks."
},
"linkingId": {
"description": "Specify an ID for [linking multiple views](http://gosling-lang.org/docs/user-interaction#linking-views)",
"type": "string"
},
"orientation": {
"$ref": "#/definitions/Orientation",
"description": "Specify the orientation."
},
"outerRadius": {
"description": "Specify the outer radius of tracks when `{\"layout\": \"circular\"}`.",
"type": "number"
},
"overlayOnPreviousTrack": {
"type": "boolean"
},
"prerelease": {
"additionalProperties": false,
"description": "internal",
"type": "object"
},
"spacing": {
"description": "- If `{\"layout\": \"linear\"}`, specify the space between tracks in pixels;\n\n- If `{\"layout\": \"circular\"}`, specify the space between tracks in percentage ranging from 0 to 100.",
"type": "number"
},
"startAngle": {
"description": "Specify the start angle (in the range of [0, 360]) of circular tracks (`{\"layout\": \"circular\"}`).",
"type": "number"
},
"static": {
"description": "Whether to disable [Zooming and Panning](http://gosling-lang.org/docs/user-interaction#zooming-and-panning), __Default:__ `false`.",
"type": "boolean"
},
"style": {
"$ref": "#/definitions/Style",
"description": "Define the [style](http://gosling-lang.org/docs/visual-channel#style-related-properties) of multive views. Will be overriden by the style of children elements (e.g., view, track)."
},
"subtitle": {
"type": "string"
},
"title": {
"description": "If defined, will show the textual label on the left-top corner of a track.",
"type": "string"
},
"width": {
"description": "Specify the track width in pixels.",
"type": "number"
},
"xAxis": {
"$ref": "#/definitions/AxisPosition",
"description": "not supported"
},
"xDomain": {
"anyOf": [
{
"$ref": "#/definitions/DomainInterval"
},
{
"$ref": "#/definitions/DomainChrInterval"
},
{
"$ref": "#/definitions/DomainChr"
}
]
},
"xOffset": {
"description": "Specify the x offset of views in the unit of pixels",
"type": "number"
},
"yOffset": {
"description": "Specify the y offset of views in the unit of pixels",
"type": "number"
},
"zoomLimits": {
"$ref": "#/definitions/ZoomLimits"
}
},
"required": [
"data",
"height",
"width"
],
"type": "object"
},
"DataTransform": {
"anyOf": [
{
"$ref": "#/definitions/FilterTransform"
},
{
"$ref": "#/definitions/StrConcatTransform"
},
{
"$ref": "#/definitions/StrReplaceTransform"
},
{
"$ref": "#/definitions/LogTransform"
},
{
"$ref": "#/definitions/DisplaceTransform"
},
{
"$ref": "#/definitions/ExonSplitTransform"
},
{
"$ref": "#/definitions/GenomicLengthTransform"
},
{
"$ref": "#/definitions/CoverageTransform"
},
{
"$ref": "#/definitions/CombineMatesTransform"
},
{
"$ref": "#/definitions/JSONParseTransform"
}
]
},
"Datum": {
"additionalProperties": {
"type": [
"number",
"string"
]
},
"description": "Values in the form of JSON.",
"type": "object"
},
"DisplaceTransform": {
"additionalProperties": false,
"properties": {
"boundingBox": {
"additionalProperties": false,
"properties": {
"endField": {
"description": "The name of a quantitative field that represents the end position.",
"type": "string"
},
"groupField": {
"description": "The name of a nominal field to group rows by in prior to piling-up.",
"type": "string"
},
"isPaddingBP": {
"description": "Whether to consider `padding` as the bp length.",
"type": "boolean"
},
"padding": {
"description": "The padding around visual lements. Either px or bp",
"type": "number"
},
"startField": {
"description": "The name of a quantitative field that represents the start position.",
"type": "string"
}
},
"required": [
"startField",
"endField"
],
"type": "object"
},
"maxRows": {
"description": "Specify maximum rows to be generated (default has no limit).",
"type": "number"
},
"method": {
"$ref": "#/definitions/DisplacementType",
"description": "A string that specifies the type of diseplancement."
},
"newField": {
"type": "string"
},
"type": {
"const": "displace",
"type": "string"
}
},
"required": [
"type",
"boundingBox",
"method",
"newField"
],
"type": "object"
},
"Displacement": {
"additionalProperties": false,
"properties": {
"padding": {
"type": "number"
},
"type": {
"$ref": "#/definitions/DisplacementType"
}
},
"required": [
"type"
],
"type": "object"
},
"DisplacementType": {
"enum": [
"pile",
"spread"
],
"type": "string"
},
"DomainChr": {
"additionalProperties": false,
"properties": {
"chromosome": {
"$ref": "#/definitions/Chromosome"
}
},
"required": [
"chromosome"
],
"type": "object"
},
"DomainChrInterval": {
"additionalProperties": false,
"properties": {
"chromosome": {
"$ref": "#/definitions/Chromosome"
},
"interval": {
"items": [
{
"type": "number"
},
{
"type": "number"
}
],
"maxItems": 2,
"minItems": 2,
"type": "array"
}
},
"required": [
"chromosome",
"interval"
],
"type": "object"
},
"DomainGene": {
"additionalProperties": false,
"properties": {
"gene": {
"anyOf": [
{
"type": "string"
},
{
"items": [
{
"type": "string"
},
{
"type": "string"
}
],
"maxItems": 2,
"minItems": 2,
"type": "array"
}
]
}
},
"required": [
"gene"
],
"type": "object"
},
"DomainInterval": {
"additionalProperties": false,
"properties": {
"interval": {
"items": [
{
"type": "number"
},
{
"type": "number"
}
],
"maxItems": 2,
"minItems": 2,
"type": "array"
}
},
"required": [
"interval"
],
"type": "object"
},
"ExonSplitTransform": {
"additionalProperties": false,
"properties": {
"fields": {
"items": {
"additionalProperties": false,
"properties": {
"chrField": {
"type": "string"
},
"field": {
"type": "string"
},
"newField": {
"type": "string"
},
"type": {
"$ref": "#/definitions/FieldType"
}
},
"required": [
"field",
"type",
"newField",
"chrField"
],
"type": "object"
},
"type": "array"
},
"flag": {
"additionalProperties": false,
"properties": {
"field": {
"type": "string"
},
"value": {
"type": [
"number",
"string"
]
}
},
"required": [
"field",
"value"
],
"type": "object"
},
"separator": {
"type": "string"
},
"type": {
"const": "exonSplit",
"type": "string"
}
},
"required": [
"type",
"separator",
"flag",
"fields"
],
"type": "object"
},
"FieldType": {
"enum": [
"genomic",
"nominal",
"quantitative"
],
"type": "string"
},
"FilterTransform": {
"anyOf": [
{
"$ref": "#/definitions/OneOfFilter"
},
{
"$ref": "#/definitions/RangeFilter"
},
{
"$ref": "#/definitions/IncludeFilter"
}
]
},
"FlatTracks": {
"additionalProperties": false,
"properties": {
"assembly": {
"$ref": "#/definitions/Assembly",
"description": "A string that specifies the genome builds to use. Currently support `\"hg38\"`, `\"hg19\"`, `\"hg18\"`, `\"hg17\"`, `\"hg16\"`, `\"mm10\"`, `\"mm9\"`, and `\"unknown\"`.\n\n__Note:__: with `\"unknown\"` assembly, genomic axes do not show chrN: in labels."
},
"centerRadius": {
"description": "Proportion of the radius of the center white space.\n\n__Default:__ 0.3",
"type": "number"
},
"layout": {
"$ref": "#/definitions/Layout",