.. This document is auto-generated by the gosling-gallery extension. Do not modify directly.

.. _gallery_genes:

Gene Annotation
===============

Re-implementation of `Higlass gene-annotations track`_

.. _Higlass gene-annotations track: https://docs.higlass.io/track_types.html#gene-annotations

.. gosling-plot::
    :code-below:

    
    import gosling as gos

    genes = gos.beddb(
        url="https://server.gosling-lang.org/api/v1/tileset_info/?d=gene-annotation",
        genomicFields=[
          {"index": 1, "name": "start"},
          {"index": 2, "name": "end"}
        ],
        valueFields=[
          {"index": 5, "name": "strand", "type": "nominal"},
          {"index": 3, "name": "name", "type": "nominal"}
        ],
        exonIntervalFields=[
          {"index": 12, "name": "start"},
          {"index": 13, "name": "end"}
        ]
    )

    base = gos.Track(genes).encode(
        row=gos.Row("strand:N", domain=["+", "-"]),
        color=gos.Color("strand:N", domain=["+", "-"], range=["#7585FF", "#FF8A85"]),
        tooltip=["start:G", "end:G", "strand:N", "name:N"],
    ).properties(
        title="Genes | hg38",
    )

    plusGeneHead = base.mark_triangleRight(align="left").encode(
        x=gos.X("end:G", axis="top"),
        size=gos.value(15)
    ).transform_filter(
        field="type", oneOf=["gene"]
    ).transform_filter(
        field="strand", oneOf=["+"]
    )

    minusGeneHead = base.mark_triangleLeft(align="right").encode(
        x=gos.X("start:G", axis="top"),
        size=gos.value(15)
    ).transform_filter(
        field="type", oneOf=["gene"]
    ).transform_filter(
        field="strand", oneOf=["-"]
    )

    geneLabel = base.mark_text(dy=15).encode(
        x=gos.X("start:G", axis="top"),
        xe="end:G",
        text="name:N",
        size=gos.value(15)
    ).transform_filter(
        field="type", oneOf=["gene"]
    ).visibility_lt(
        measure="width",
        threshold="|xe-x|",
        transitionPadding=10,
        target="mark",
    )

    exon = base.mark_rect().encode(
        x=gos.X("start:G", axis="top"),
        xe="end:G",
        size=gos.value(15)
    ).transform_filter(
        field="type", oneOf=["exon"]
    )

    plusGeneRange = base.mark_rule(linePattern={"type": "triangleRight", "size": 5}).encode(
        x=gos.X("start:G", axis="top"),
        xe="end:G",
        strokeWidth=gos.value(3),
    ).transform_filter(
        field="type", oneOf=["gene"]
    ).transform_filter(
        field="strand", oneOf=["+"]
    )

    minusGeneRange = base.mark_rule(linePattern={"type": "triangleLeft", "size": 5}).encode(
        x=gos.X("start:G", axis="top"),
        xe="end:G",
        strokeWidth=gos.value(3),
    ).transform_filter(
        field="type", oneOf=["gene"]
    ).transform_filter(
        field="strand", oneOf=["-"]
    )

    gos.overlay(
        plusGeneRange, minusGeneRange, exon, plusGeneHead, minusGeneHead, geneLabel
    ).properties(
        width=725, height=100,
        title="Gene Annotation",
        xDomain=gos.GenomicDomain(chromosome="chr1", interval=[103400000, 103700000]),
        assembly="hg38",
        layout="linear",
        centerRadius=0.7,
    )