Help me plot exons of genes

[andreaswallberg]

Hi everyone!

I am playing around with the GFF parsing and gene plotting capabilities of Gosling and I struggle to visualize exons after reading in a GFF file. Essentially, I would like to plot the exon blocks at the same height as the start and end marks of the genes ("15"), but the dataTransform does not seem to catch the type "exon" in the relevant code.

Here are my tracks:

      "tracks": [
        {
          "dataTransform": [
            {"type": "filter", "field": "type", "oneOf": ["gene"]}
          ],
          "mark": "rule",
          "x": {"field": "start", "type": "genomic"},
          "xe": {"field": "end", "type": "genomic"},
          "strokeWidth": {"value": 3}
        },
        {
          "dataTransform": [
            {"type": "filter", "field": "type", "oneOf": ["gene"]},
          ],
          "mark": "rect",
          "x": {"field": "start", "type": "genomic"},
          "size": {"value": 15},
        },
        {
          "dataTransform": [
            {"type": "filter", "field": "type", "oneOf": ["gene"]},
          ],
          "mark": "rect",
          "x": {"field": "end", "type": "genomic"},
          "size": {"value": 15},
        },
        {
          "dataTransform": [
            {"type": "filter", "field": "type", "oneOf": ["gene"]}
          ],
          "mark": "text",
          "text": {"field": "ID", "type": "nominal"},
          "x": {"field": "start", "type": "genomic"},
          "xe": {"field": "end", "type": "genomic"},
          "style": {"dy": -10}
        },
        {
          "dataTransform": [
            {"type": "filter", "field": "type", "oneOf": ["exon"]}
          ],
          "mark": "rect",
          "x": {"field": "start", "type": "genomic"},
          "xe": {"field": "end", "type": "genomic"},
          "strokeWidth": {"value": 15}
        },
      ],

If I flip "oneOf": ["exon"]} to "oneOf": ["gene"]} then dataTransform catches it but of course plots the whole gene at that width, instead of each individual exon.

Is "exon" not a "type"?

Or does the GFF parser (in HiGlass?) throw away all types that are not "gene" somewhere upstream?