Custom colors when adding a MultiQuantitativeTrack JSON through jbrowse CLI

[weber8thomas]

Hi everyone,

I was curious to know if it would be possible to customise colors directly on a JSON added through jbrowse CLI (through jbrowse add-track-json). I would like to programatically assign different colors to the two tracks of my MultiQuantitativeTrack.

{
    "type": "MultiQuantitativeTrack",
    "trackId": "BM510x04_PE20301",
    "name": "BM510x04_PE20301",
    "assemblyNames": [
        "chr17"
    ],
    "adapter": {
        "type": "MultiWiggleAdapter",
        "subadapters": [
            {
                "type": "BigWigAdapter",
                "name": "BM510x04_PE20301-C.bigWig",
                "bigWigLocation": {
                    "uri": "http://127.0.0.1:9000/depictio-bucket/BM510x04_PE20301-C.bigWig",
                    "locationType": "UriLocation"
                }
            },
            {
                "type": "BigWigAdapter",
                "name": "BM510x04_PE20301-W.bigWig",
                "bigWigLocation": {
                    "uri": "http://127.0.0.1:9000/depictio-bucket/BM510x04_PE20301-W.bigWig",
                    "locationType": "UriLocation"
                }
            }
        ]
    },
    "displays": [
        {
            "type": "MultiLinearWiggleDisplay",
            "displayId": "BM510x04_PE20301-sessionTrack-MultiLinearWiggleDisplay",
            "defaultRendering": "xyplot"
        }
    ]
}

I already tried to modify directly the display section, as well as adding a XYPlotRenderer, but nothing worked yet.

Many thanks in advance for your help!

Cheers, Thomas

[cmdcolin]

multiwiggleadapter is actually a case where you can specify the color in the adapter config section

*many other track types are not like this and specify the color in the "display" config for example, but there is a shortcut for multiwiggleadapter to specify

{
      "type": "MultiQuantitativeTrack",
      "trackId": "example",
      "name": "example",
      "assemblyNames": ["hg19"],
      "adapter": {
        "type": "MultiWiggleAdapter",
        "subadapters": [
          {
            "type": "BigWigAdapter",
            "color": "purple",
            "name":"k1",
            "bigWigLocation": {"uri": "https://www.encodeproject.org/files/ENCFF055ZII/@@download/ENCFF055ZII.bigWig"}
          },
          {
            "type": "BigWigAdapter",
            "color": "green",
            "name":"k2",
            "bigWigLocation": {"uri": "https://www.encodeproject.org/files/ENCFF826HEW/@@download/ENCFF826HEW.bigWig"}
          }
        ]
      }
    }

[cmdcolin]

also I think that there is actually not a way to specify it in the display config currently. if that is of interest let me know but hopefully that helps

[cmdcolin]

finally, this is not apparently in the docs, so will update :)

[weber8thomas]

Many thanks @cmdcolin ! Works like a charm :)