Datahub¶

A datahub is a JSON file descibing a set of tracks in the browser. A datahub file is an array of tracks, which are also defined in JSON syntax:

[
    {
    "type": "track_type1",
    "name": "track_name1",
    "url": "track_url1",
    "options": {
        "color": "red"
        }
    },
    {
    "type": "track_type2",
    "name": "track_name2",
    "url": "track_url2",
    "options": {
        "color": "blue"
        }
    }
]

Example data hub¶

Pasted below is an example data hub for mouse mm10:

[
    {
    "type": "bigwig",
    "url": "https://vizhub.wustl.edu/public/tmp/TW463_20-5-bonemarrow_MeDIP.bigWig",
    "name": "MeDIP",
    "options": {
        "color": "red",
        "backgroundColor":"#FFE7AB"
        },
    "metadata": {
        "sample": "bone",
        "assay": "MeDIP"
        }
    },
    {
    "type": "bigwig",
    "url": "https://vizhub.wustl.edu/public/tmp/TW551_20-5-bonemarrow_MRE.CpG.bigWig",
    "name": "MRE",
    "options": {
        "color": "blue",
        "backgroundColor":"#C0E3CC"
        },
    "metadata": {
        "sample": "bone",
        "assay": "MRE"
        }
    }
]

Example bigWig track¶

{
    "type": "bigwig",
    "name": "example bigwig",
    "url": "https://vizhub.wustl.edu/hubSample/hg19/GSM429321.bigWig",
    "options": {
        "color": "blue"
    }
}

Example methylC track¶

{
  "type": "methylc",
  "name": "H1",
  "url": "https://vizhub.wustl.edu/public/hg19/methylc2/h1.liftedtohg19.gz",
  "options": {
    "label": "Methylation",
    "colorsForContext": {
      "CG": { "color": "#648bd8", "background": "#d9d9d9" },
      "CHG": { "color": "#ff944d", "background": "#ffe0cc" },
      "CHH": { "color": "#ff00ff", "background": "#ffe5ff" }
    },
    "depthColor": "#01E9FE"
  },
}

Example categorical track¶

{
  "type": "categorical",
  "name": "ChromHMM",
  "url": "https://egg.wustl.edu/d/hg19/E017_15_coreMarks_dense.gz",
  "options": {
      "category": {
          "1": {"name": "Active TSS", "color": "#ff0000"},
          "2": {"name": "Flanking Active TSS", "color": "#ff4500"},
          "3": {"name": "Transcr at gene 5' and 3'", "color": "#32cd32"},
          "4": {"name": "Strong transcription", "color": "#008000"},
          "5": {"name": "Weak transcription", "color": "#006400"},
          "6": {"name": "Genic enhancers", "color": "#c2e105"},
          "7": {"name": "Enhancers", "color": "#ffff00"},
          "8": {"name": "ZNF genes & repeats", "color": "#66cdaa"},
          "9": {"name": "Heterochromatin", "color": "#8    a91d0"},
          "10": {"name": "Bivalent/Poised TSS", "color": "#cd5c5c"},
          "11": {"name": "Flanking Bivalent TSS/Enh", "color": "#e9967a"},
          "12": {"name": "Bivalent Enhancer", "color": "#bdb76b"},
          "13": {"name": "Repressed PolyComb", "color": "#808080"},
          "14": {"name": "Weak Repressed PolyComb", "color": "#c0c0c0"},
          "15": {"name": "Quiescent/Low", "color": "#ffffff"}
      }
  }
}

Supported options: backgroundColor, color, color2, yScale, yMax, and yMin.

Example longrange track¶

{
    "type": "longrange",
    "name": "ES-E14 ChIA-PET",
    "url": "https://egg.wustl.edu/d/mm9/GSE28247_st3c.gz"
}

Example bigInteract track¶

{
    "type": "biginteract",
    "name": "test bigInteract",
    "url": "https://epgg-test.wustl.edu/dli/long-range-test/interactExample3.inter.bb"
}

Example repeatmasker track¶

{
    "type": "repeatmasker",
    "name": "RepeatMasker",
    "url": "https://vizhub.wustl.edu/public/mm10/rmsk16.bb"
}

Example geneAnnotation track¶

{
    "type": "geneAnnotation",
    "name": "refGene",
    "genome": "mm10"
}

Note

Please specify the genome attibute for gene annotation tracks.

Example bigbed track¶

{
    "type": "bigbed",
    "name": "test bigbed",
    "url": "https://vizhub.wustl.edu/hubSample/hg19/bigBed1"
}

Example bed track¶

{
    "type": "bed",
    "name": "mm10 bed",
    "url": "https://epgg-test.wustl.edu/d/mm10/mm10_cpgIslands.bed.gz"
}

Example refbed track¶

{
    "type": "refbed",
    "name": "mm10 gencode basic",
    "url": "https://vizhub.wustl.edu/public/tmp/gencodeM18_load_basic_Gene.bed.gz",
    "options": {
            "categoryColors": {
                "coding": "rgb(101,1,168)",
                "nonCoding": "rgb(1,193,75)",
                "pseudo": "rgb(230,0,172)",
                "problem": "rgb(224,2,2)",
                "other":"rgb(128,128,128)"
            }
        }
}

Note

categoryColors designates colors for the gene type as indicated in the 9th column. The default scheme is shown above for the five classes created by the Converting_Gencode_or_Ensembl_GTF_to_refBed.bash script, but any number of categories can be defined.

Example HiC track¶

{
    "type": "hic",
    "name": "test hic",
    "url": "https://epgg-test.wustl.edu/dli/long-range-test/test.hic",
    "options": {
        "displayMode": "arc"
    }
}

Example cool track¶

{
    "type": "cool",
    "name": "Aiden et al. (2009) GM06900 HINDIII 1kb",
    "url": "Hyc3TZevQVm3FcTAZShLQg",
    "options": {
        "displayMode": "arc"
    }
}

Note

please note we are using the uuid Hyc3TZevQVm3FcTAZShLQg here from higlass API server instead of a file URL to represent a cool track.

Example genomealign track¶

{
    "name": "hg19 to mm10 alignment",
    "type": "genomealign",
    "metadata": {
        "genome": "mm10"
    }
}

Example Ruler track¶

{
    "type": "ruler",
    "name": "Ruler"
}

Track properties¶

type¶

Requried. type specifies the track type, currently supported track types:

bigWig
bedGraph
methylC
categorical
hic
bed
bigbed
refbed
repeatmasker
geneAnnotation
genomealign
longrange
bigInteract
ruler

Note

type is case insensitive.

name¶

Requried. name specifies the track name used internally by the browser. It is also displayed as the track legend if no label speficied. Value can be any string.

label¶

Optional. label specifies the track legend displayed in the browser. It overrides the name arrtibute. Value can be any string.

url¶

Requried. url contains the URL to the track file and needs to be HTTP or HTTPS location string.

Important

A url is requried for all the tracks in binary format. Gene annotaion tracks, like refGene, do not need a url as they are stored in the Mongo database. Additional annotation tracks, such as the ruler track, also do not need a url.

Caution

Each user-provided url must link to a publically available website, without password protection, so that the browser can read in the file.

metadata¶

Optional. An object specifying the metadata of the track.

In this basic example the value of each metadata term is a string.

"metadata": {
    "sample": "bone",
    "assay": "MRE"
}

This example public Roadmap data hub has more complex metadata definitions and makes use of a list of strings to build a hierarchical structure.

{
    "url": "https://egg.wustl.edu/d/hg19/GSM997242_1.bigWig",
    "metadata": {
        "Sample": [
            "Adult Cells/Tissues",
            "Blood",
            "Other blood cells",
            "CD4+_CD25-_Th_Primary_Cells"
        ],
        "Donor": [
            "Donor Identifier",
            "Donor_332"
        ],
        "Assay": [
            "Epigenetic Mark",
            "Histone Mark",
            "H3",
            "H3K9",
            "H3K9me3"
        ],
        "Institution": [
            "Broad Institute"
        ]
    },
    "type": "bigwig",
    "options": {
        "color": "rgb(159,0,72)"
    },
    "name": "H3K9me3 of CD4+_CD25-_Th_Primary_Cells"
}

The list of metadata is ordered from more generic to more specific and helps build the facet table hierarchy making the search and filter functions in track table easier.

details¶

Optional. If you want to add more information for each track then the details attribute is helpful. After right clicking on the track you can click More Information and see the details, url, and metadata for each track in the dropdown menu.

"details": {
    "data source": "Roadmap Project",
    "date collected": "May 7 2016"
}

options¶

Optional. All track render options are placed in an object called options. This object can have the following properties:

color¶

color is used to define the color for each track. A color name, RGB values, or hex color code can be used. For more about color name or RGB please see https://www.w3schools.com/css/css_colors.asp.

color2¶

color2 is used to define the color for negative values from the track data. The default is the same as color.

backgroundColor¶

backgroundColor defines the background color of the track.

height¶

height controls the height of the track which is specified as a number and displayed in pixels.

yScale¶

yScale allows you to configure the track’s y-scale. Options include auto or fixed. auto sets the y-scale from 0 to the max value of values in the view region for a given track. fixed means you can specify the minimal and maximal value.

yMax¶

yMax is used to define the maximum value of a track’s y-axis. Value is number.

yMin¶

yMin is used to define the minimum value of a track’s y-axis. Value is number.

Important

If you need the track to be in fixed scale, you need to specify yScale to fixed besides of set yMax and yMin.

colorAboveMax¶

colorAboveMax defines the color displayed when a fixed yScale is used and a value exceeds the yMax defined.

color2BelowMin¶

color2BelowMin defines the color displayed when a fixed yScale is used and a value is below the yMin defined.

displayMode¶

displayMode specifies display mode for each tracks. Different tracks have different display modes as listed below.

type	display mode
bigWig	auto, bar, heatmap
bedGraph	auto, bar, heatmap
geneAnnotation	full, density
HiC	arc, heatmap
genomealign	rough, fine