README.md

Gosling.js Example w/o HiGlass Server

For many file formats Gosling can parse the data directly from a web server without the need to request tiles from a HiGlass server. The list of "serverless" file formats can be found here:

https://github.com/gosling-lang/gosling-docs/blob/master/docs/Data.md#plain-datasets

gosling.js

{
  "title": "Circos w/o HiGlass Server and Circles",
  "description": "http://circos.ca/intro/genomic_data/",
  "layout": "linear",
  "static": false,
  "spacing": 1,
  "centerRadius": 0.3,
  "tracks": [
    {
      "data": {
        "url": "https://raw.githubusercontent.com/sehilyi/gemini-datasets/master/data/UCSC.HG38.Human.CytoBandIdeogram.csv",
        "type": "csv",
        "chromosomeField": "Chromosome",
        "genomicFields": ["chromStart", "chromEnd"]
      },
      "mark": "rect",
      "color": {
        "field": "Stain",
        "type": "nominal",
        "domain": [
          "gneg",
          "gpos25",
          "gpos50",
          "gpos75",
          "gpos100",
          "gvar",
          "acen"
        ],
        "range": [
          "white",
          "#D9D9D9",
          "#979797",
          "#636363",
          "black",
          "#F0F0F0",
          "#8D8D8D"
        ]
      },
      "x": {"field": "chromStart", "type": "genomic"},
      "xe": {"field": "chromEnd", "type": "genomic"},
      "stroke": {"value": "lightgray"},
      "strokeWidth": {"value": 0.5},
      "width": 600,
      "height": 30
    },
    {
      "data": {
        "url": "https://raw.githubusercontent.com/vigsterkr/circos/master/data/5/segdup.txt",
        "type": "csv",
        "headerNames": ["id", "chr", "p1", "p2"],
        "chromosomePrefix": "hs",
        "chromosomeField": "chr",
        "genomicFields": ["p1", "p2"],
        "separator": " ",
        "longToWideId": "id"
      },
      "dataTransform": {
        "filter": [{"field": "chr", "oneOf": ["hs1"], "not": true}]
      },
      "mark": "link",
      "x": {"field": "p1", "type": "genomic"},
      "xe": {"field": "p1_2", "type": "genomic"},
      "x1": {"field": "p2", "type": "genomic"},
      "x1e": {"field": "P2_2", "type": "genomic"},
      "stroke": {"value": "lightgray"},
      "strokeWidth": {"value": 1},
      "opacity": {"value": 0.4},
      "width": 600,
      "height": 400
    },
    {
      "data": {
        "url": "https://raw.githubusercontent.com/vigsterkr/circos/master/data/5/segdup.txt",
        "type": "csv",
        "headerNames": ["id", "chr", "p1", "p2"],
        "chromosomePrefix": "hs",
        "chromosomeField": "chr",
        "genomicFields": ["p1", "p2"],
        "separator": " ",
        "longToWideId": "id"
      },
      "dataTransform": {"filter": [{"field": "chr", "oneOf": ["hs1"]}]},
      "mark": "link",
      "x": {"field": "p1", "type": "genomic"},
      "xe": {"field": "p1_2", "type": "genomic"},
      "x1": {"field": "p2", "type": "genomic"},
      "x1e": {"field": "P2_2", "type": "genomic"},
      "stroke": {
        "field": "chr_2",
        "type": "nominal",
        "range": [
          "#E79F00",
          "#029F73",
          "#0072B2",
          "#CB7AA7",
          "#D45E00",
          "#57B4E9",
          "#EFE441"
        ]
      },
      "strokeWidth": {"value": 1.5},
      "opacity": {"value": 0.4},
      "width": 700,
      "height": 300,
      "overlayOnPreviousTrack": true
    }
  ]
}