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

.. _gallery_circos:

Circos
======

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

    
    import gosling as gos

    WIDTH = 725

    tileset = gos.vector(
        url="https://resgen.io/api/v1/tileset_info/?d=VLFaiSVjTjW6mkbjRjWREA",
        column="position",
        value="peak",
    )

    cytoband = gos.csv(
        url="https://raw.githubusercontent.com/sehilyi/gemini-datasets/master/data/UCSC.HG38.Human.CytoBandIdeogram.csv",
        chromosomeField="Chromosome",
        genomicFields=["chromStart", "chromEnd"],
    )

    segdup = gos.csv(
        url="https://raw.githubusercontent.com/vigsterkr/circos/master/data/5/segdup.txt",
        headerNames=["id", "chr", "p1", "p2"],
        chromosomePrefix="hs",
        chromosomeField="chr",
        genomicFields=["p1", "p2"],
        separator=" ",
        longToWideId="id",
    )

    bars = gos.Track(tileset).mark_bar().encode(
        x=gos.X("position:G", axis="top"),
        y=gos.Y("peak:Q", axis="right"),
        color=gos.value("#EEEDA1"),
    ).properties(width=WIDTH, height=60)

    ideogram = gos.Track(cytoband).mark_rect().encode(
        color=gos.Color("Stain:N",
            domain=["gneg", "gpos25", "gpos50", "gpos75", "gpos100", "gvar", "acen"],
            range=["white", "#D9D9D9", "#979797", "#636363", "black", "#F0F0F0", "#8D8D8D"],
        ),
        x="chromStart:G",
        xe="chromEnd:G",
        stroke=gos.value("lightgray"),
        strokeWidth=gos.value(0.5),
    ).properties(width=WIDTH, height=30)


    link_base = gos.Track(segdup).mark_withinLink().encode(
        x="p1:G",
        xe="p1_2:G",
        x1="p2:G",
        x1e="P2_2:G",
        opacity=gos.value(0.4)
    )

    colors = ["#E79F00", "#029F73", "#0072B2", "#CB7AA7", "#D45E00", "#57B4E9", "#EFE441"]

    link = gos.overlay(
        link_base
            .encode(stroke=gos.value("lightgray"), strokeWidth=gos.value(1))
            .transform_filter_not("chr", oneOf=["hs1"])
        ,
        link_base
            .encode(stroke=gos.Stroke("chr_2:N", range=colors), strokeWidth=gos.value(1.5))
            .transform_filter("chr", oneOf=["hs1"])
    )

    gos.stack(bars, ideogram, link).properties(
        title="Circos",
        description="http://circos.ca/intro/genomic_data/",
        layout="circular",
        static=True,
        spacing=1,
        centerRadius=0.3,
    )