View Configs

Viewconfs specify exactly what a HiGlass view should show. They contain a list of the data sources, visualization types, visible region as well as searching and styling options.

Show a specific genomic location

Say we want to have a viewconf which was centered on the gene OSR1. Its location is roughly between positions 19,500,000 and 19,600,000 on chromosome 7 of the hg19 assembly. So what should initialXDomain be set to in order to show this gene?

Because initialXDomain accepts absolute coordinates calculated by concatenating chromosomes according to a certain order, we need to calculate what chr2:19,500,000 and chr2:196,000,000 are in absolute coordinates.

To do this we will assume a chromosome ordering consisting of chr1, chr2, … This means that we need to take the length of chr1 in hg19, which is 249,250,621 base pairs, and add our positions to that, yielding positions 268,750,621 and 268,850,621 for the initialXDomain.

The chromosome order commonly used in HiGlass for hg19 can be found in the negspy repository.

Upload a viewconf to the server

A local viewconf can be sent to the server by sending a POST request. Make sure the actual viewconf is wrapped in the viewconf section of the posted json (e.g. {“viewconf”: myViewconf}):

curl -H "Content-Type: application/json" \
     -X POST \
     -d '{"viewconf": {"editable": true, "zoomFixed": false, "trackSourceServers": ["/api/v2", "http://higlass.io/api/v1"], "exportViewUrl": "/api/v1/viewconfs/", "views": [{"tracks": {"top": [], "left": [], "center": [], "right": [], "bottom": []}, "initialXDomain": [243883495.14563107, 2956116504.854369], "initialYDomain": [804660194.1747572, 2395339805.825243], "layout": {"w": 12, "h": 12, "x": 0, "y": 0, "i": "EwiSznw8ST2HF3CjHx-tCg", "moved": false, "static": false}, "uid": "EwiSznw8ST2HF3CjHx-tCg"}], "zoomLocks": {"locksByViewUid": {}, "locksDict": {}}, "locationLocks": {"locksByViewUid": {}, "locksDict": {}}, "valueScaleLocks": {"locksByViewUid": {}, "locksDict": {}}}}' http://localhost:8989/api/v1/viewconfs/

Edit the view config online

The view config can be directly adjusted in the browser to give an easy access to all available options that might not otherwise be accessible through the user interface yet. To open the editor click on _cog wheel_ icon in the view header and select _Edit view config_.

The editor support a couple of keyboard shortcuts to make editing fast:

  • ``CMD (or CTRL) + S `` to save and apply the view config
  • ESC to claose the modl and to undue all (saved but not finalized) changes introduced while editing the view config.
  • CMD (or CTRL) + Enter to save, apply, and finalize changes and close the modal
  • Hold ALT for 1 second to temporarily hide the modal. The modal will reappear as soon as you release ALT.

For example, here is a recipe for fixing heatmap value scale limits which is useful when browsing Hi-C data with a linear color scale because of its very high dynamic range. First, locate the description of the heatmap track you want to edit and find the options dictionary.

{
...
"type": "heatmap",
"options": {
    "name": "My Hi-C map",
    ...
    "heatmapValueScaling": "log",
    "showMousePosition": false,
    ...
},
...
}

Then set heatmapValueScaling to "linear" if not set already and add two additional entries: valueScaleMin and valueScaleMax.

{
...
"type": "heatmap",
"options": {
    "name": "My Hi-C map",
    ...
    "heatmapValueScaling": "linear",
    "valueScaleMin": 0.0,
    "valueScaleMax": 0.02,
    "showMousePosition": false,
    ...
},
...
}

Finally, save to apply the changes.

Viewconf Structure

The viewconf defines which data is shown by HiGlass and how it is arranged. It is organized into views, tracks and other metadata. This section will focus on the root-level metadata. The sections below will delve into views and tracks.

editable: [true | false] (default: true)
viewEditable: [true | false] (default: true)
tracksEditable: [true | false] (default: true)

The property viewEditable specifies whether this viewconf will have a view header and the property viewEditable determines if tracks have a context menu. editable will force both properties to either be true or false.

"trackSourceServers": [
  "http://higlass.io/api/v1",
  "http://localhost:8989/api/v1"
],

Where should the list of available tracks be pulled from? The field trackSourceServers at the root level of the viewconf tells higlass where it can find tracks to load. If you have a local instance running, then http://localhost:8989/api/v1 should be included. Our public instance at http://higlass.io also provides access to a number of public datasets.

{
    "exportViewUrl": "/api/v1/viewconfs",
}

The exportViewUrl field in the viewconf specifies which endpoint should be used to store exported viewconfs. This endpoint stores exported viewconfs in its database, assigns them a uid, and makes them accessible through its API at /api/v1/viewconfs/uid/. The default points to a url on the same server that is hosting the higlass application. It can also be changed to point to an external location (i.e. ‘http://higlass.my.department.com/api/v1/viewconfs’).

Views

Views are placed within the top level of the viewconf and arranged in a list:

{
  views: [
    {
      ...
    }
  ]
}

The rest of this section refers to elements within the individual view sections.

UIDs

UID stands for unique identifier. Every view and track in the higlass viewconf has a UID. If it’s not specified in the viewconf it’s randomly generated by the client when the view is created.

initialXDomain and initialYDomain

The fields contain the initial coordinates which are displayed when HiGlass first loads the viewconf. If the initialYDomain is not present, it is set to equal the initialXDomain. If that isn’t present either, both are assigned values of [0,1]].

{
    views: [
        {
              "uid": "AhI0wMP6ScybnFp6BmLuPQ",
              "initialXDomain": [
                973907089.1176914,
                1196247735.9596405
              ],
              "initialYDomain": [
                -12281154450.083118,
                -12145323104.213125
              ],
            "genomePositionSearchBox": {
                "autocompleteServer": "http://higlass.io/api/v1",
                "autocompleteId": "OHJakQICQD6gTD7skx4EWA",
                "chromInfoServer": "http://higlass.io/api/v1",
                "chromInfoId": "hg19",
                "visible": true
            }
    ]
}

zoomLimits

The field contains limits that controll the extend to which zooming is possible within a view. In the example below, zooming in is not possible beyond 200bp. If one of the items in the array is null, zooming is unrestricted in the corresponding direction. If the field is not present in the viewconf, it defaults to [1, null].

{
    views: [
        {
              "uid": "AhI0wMP6ScybnFp6BmLuPQ",
              "initialXDomain": [
                973907089.1176914,
                1196247735.9596405
              ],
              "initialYDomain": [
                -12281154450.083118,
                -12145323104.213125
              ],
              "zoomLimits": [
                200,
                3400000000
              ],
    ]
}

trackSourceServers

The field trackSourceServers at the root level of the viewconf tells higlass where it can find tracks to load. If you have a local instance running, then http://localhost:8989/api/v1 should be included. Our public instance at http://higlass.io also provides access to a number of public datasets.

{
  "trackSourceServers": [
    "http://higlass.io/api/v1",
    "http://localhost:8989/api/v1"
  ],
}

exportViewUrl

The exportViewUrl field in the viewconf specifies which server should be used to store exported viewconfs. This server stores exported viewconfs in its database, assigns them a uid, and makes them accessible through its API at /api/v1/viewconfs/uid/.

{
    "exportViewUrl": "/api/v1/viewconfs",
}

Tracks

Tracks can be placed into five distinct areas: top, bottom, left, right or center. The location of the track determines what type of data can be shown in it. Center tracks are used to show data that can be zoomed along two axes. Horizontal (top, bottom) and vertical (left, right) are used to show data that can be zoomed along a single axis.

Each set of tracks is placed within a view.

{
  "views": [
    {
      "tracks": {
        "top": [],
        "left": [],
        "center": [],
        "bottom": [],
        "right": []
      },
    }
  ],
}

Tracks can load data from two sources: data stored on a higlass server, ie, identified by a server and tilesetUid, or data stored at an http-accessible url and read through a higlass server. The latter approach is still currently experimental.

Using tilesetUid

The normal method of retrieving data is from a higlass server using a tilesetUid. The tilesetUid identifies a dataset on the server. It is loaded using the ingest_tileset command demonstrated in the data preparation section. To view this type of data, the track entry in the viewconf needs to contain server and tilesetUid entries:

{
  "type": "heatmap",
  "server": "http://higlass.io/api/v1",
  "tilesetUid": "default",
}

Using data

In addition to using tilesetUid to specify a data source, the data section can be used to configure other data sources or to create data sources consisting of multiple tilesets, such as one matrix divided by another.

Genbank files

A Genbank file data source will load a complete genbank file from a either text or remote URL and serve that as a gene-annotations datatype. See the horizontal-gene-annotations section for an example of a track type that can be used with Genbank files.

{
  "data": {
    "type": "genbank",
    "url": "https://pkerp.s3.amazonaws.com/public/GCA_000010365.1_ASM1036v1_genomic.gbff.gz"
  }
}

The specify the Genbank as text, replace the url field with text:

{
  "data": {
    "type": "genbank",
    "text": "LOCUS       AP009180              159662 bp    DNA..."
  }
}

Note The Genbank data sources is limited in its detail. It currently only displays genes and the names of genes. More extensive support for gene annotations (e.g. exons) should be added in the higlass/app/scripts/data-fetchers/genbank-fetcher.js file.

Other files

The second method of obtaining data is from a http-accessible url. We still need a compatible server to load data from the url and convert it to tiles, but we don’t need to explicitly register the data with the server. This can be done automatically by the client as long as it has an object with the url, server and filetype properties in the data property of the track config.

{
  "type": "vector",
  "server": "http://my-higlass.io/api/v1",
  "url": "http://hgdownload.cse.ucsc.edu/goldenpath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878InputStdSig.bigWig",
  "filetype": "bigwig"
}

Note We do not provide a compatible server “out of the box” or as part of the higlass-manage / higlass-docker distribution. To use this functionality, you have to run higlass-server directly and mount the http and httpfs directories a filesystems in userspace.

Raw tile values

We can bypass the file format and specify raw tile values using a local-tiles data fetcher. This data fetcher has to specify type: "local-tiles" and provide the tilesetInfo and tiles values. In the example below the value OHJakQICQD6gTD7skx4EWA is the equivalent of the tilesetUid used in a regular remote tile fetcher. It’s not actually used by the local tile fetcher here but it is expected to make it easy to copy and paste actual network tile requests. Because the value is not used, any string can be passed in.

data: {
  type: 'local-tiles',
  tilesetInfo: {
    OHJakQICQD6gTD7skx4EWA: {
      zoom_step: 1,
      max_length: 3137161264,
      assembly: 'hg19',
      chrom_names:
        'chr1\tchr2\tchr3\tchr4\tchr5\tchr6\tchr7\tchr8\tchr9\tchr10\tchr11\tchr12\tchr13\tchr14\tchr15\tchr16\tchr17\tchr18\tchr19\tchr20\tchr21\tchr22\tchrX\tchrY\tchrM',
      chrom_sizes:
        '249250621\t243199373\t198022430\t191154276\t180915260\t171115067\t159138663\t146364022\t141213431\t135534747\t135006516\t133851895\t115169878\t107349540\t102531392\t90354753\t81195210\t78077248\t59128983\t63025520\t48129895\t51304566\t155270560\t59373566\t16571',
      tile_size: 1024.0,
      max_zoom: 22,
      max_width: 4294967296.0,
      min_pos: [1],
      max_pos: [3137161264],
      header: '',
      name: 'Gene Annotations (hg19)',
      datatype: 'gene-annotation',
      coordSystem: 'hg19',
      coordSystem2: ''
    }
  },
  tiles: {
    'OHJakQICQD6gTD7skx4EWA.16.20101': [
      {
        xStart: 1317244685,
        xEnd: 1317481244,
        chrOffset: 1233657027,
        importance: 111.0,
        uid: 'WepfdWoIS9qSTmH9r9QUuQ',
        fields: [
          'chr7',
          '83587658',
          '83824217',
          'SEMA3A',
          '111',
          '-',
          'union_10371',
          '10371',
          'protein-coding',
          'semaphorin 3A',
          '83590686',
          '83823902',
          '83587658,83592520,83606447,83610636,83614751,83631270,83634654,83636668,83640337,83640498,83643524,83675639,83689780,83739785,83758438,83764109,83823790',
          '83591142,83592663,83606512,83610794,83614793,83631362,83634874,83636813,83640407,83640613,83643667,83675759,83689874,83739905,83758501,83764267,83824217'
        ]
      }
    ]
  }
},

Divided Tracks

The data section a track’s definition can be used to sepcify that the track should display the ratio of two datasets:

"data": {
  "type": "divided",
  "children": [
    {
      "server": "//higlass.io/api/v1",
      "tilesetUid": "H7e9Cj97SziKnltNM9pWNw"
    },
    {
      "server": "//higlass.io/api/v1",
      "tilesetUid": "Ay0kiiScSoOYKcSGKH4jjQ"
    }
  ]
}
Track options

Each track can specify a set of options defining how it will be drawn. Some of the more important ones are:

  • valueScaleMin and valueScaleMax: control the minimum and maximum values rendered by the track. If either is not defined, then it will be set according to the visible data (i.e. the minimum value of the scale will be the minimum value in the visible data and the same for the maximum)
  • showMousePosition: enables a visual crosshair at the mouse cursor’s location across the track
  • labelLeftMargin, labelRightMargin, labelTopMargin, and labelBottomMargin: add a margin to the track label. The effect is identical to CSS margin, i.e., labelLeftMargin === 10 will push the label 10px to the right if labelPosition === 'left'.
  • axisMargin: sets a margin to the very end of the plot. For example, if axisPositionHorizontal === 'left' and axisMargin === 10 then the axis will be drawn 10px from the left side of the track.
  • minHeight and minWidth: useful for tracks which are generated programmatically or otherwise edited, which have a height or width smaller than default values that may otherwise constrain rendering.
  • labelShowResolution: determines whether resolution information (for example, the text [Current data resolution: 4.096M]) is included in the track label
  • labelShowAssembly: determines whether genome assembly information (for example, the prefix ``hg19 | ``) is included in the track label

Overlay Tracks

Overlay tracks can be placed over normal tracks and can span all five distinct areas: top, bottom, left, right or center. The location of the track is determined by the tracks it should overlay. Overlay tracks by default visualize semi-transparent rectengles as annotations. Currently the only other type of overlay tracks that is supported is chromosome-grid.

Each set of tracks is placed within a view under overlays. An overlay track needs to contain an includes property. Otherwise the options depend on the type of overlay.

The extent option for overlay-annotation tracks is an array of tuples representing the start and end of each section that should be overlaid. The tuples can be either 2-tuple or 4-tuple. 2-tuple indicates that horizontal and vertical start and end coordinates are the same, 4-tuple indicates that horizontal and vertical start and end coordinates are different: [start, end] vs [x-start, x-end, y-start, y-end].

Options:

  • extent [array] (default [])
  • minWidth [number] (default 0)
  • fill [string] (default blue)
  • fillOpacity [number] (default 0.3)
  • stroke [string] (default blue)
  • strokeOpacity [number] (default 1)
  • strokeWidth [number] (default 0)
  • strokePos [string, array] (default undefined, which will drawn the stroke around the entire extent)
  • outline [string] (default white)
  • outlineOpacity [number] (default 1)
  • outlineWidth [number] (default 0)
  • outlinePos [string, array] (default undefined, which will drawn the stroke around the entire extent)

Example:

{
  views: [
    {
      overlays: [
        {
          uid: 'overlay-annotation',
          includes: ['track1Uid', 'track2Uid', 'track3Uid'],
          // Default definitions for annotations
          options: {
            extent: [
              [1000000000, 1100000000],
              [1200000000, 1300000000, 1400000, 1500000]
            ],
            minWidth: 3,
            fill: 'blue',
            fillOpacity: 0.3,
            stroke: 'yellow',
            strokeOpacity: 0.6,
            strokeWidth: 2,
            strokePos: ['left', 'right'],
            outline: 'cyan',
            outlineOpacity: 0.1337,
            outlineWidth: 1.337,
            outlinePos: 'top'
          }
        },
        {
          uid: 'overlay-chromosome-grid',
          includes: ['track1', 'track2', 'track3'],
          type: 'chromosome-grid',
          // Same definitions as the chromosome-grid track
          chromInfoPath: '//s3.amazonaws.com/pkerp/data/hg19/chromSizes.tsv',
          options: {
            lineStrokeWidth: 1,
            lineStrokeColor: 'grey'
          }
        }
      ]
    }
  ],
}