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

.. _gallery_ideograms:

Ideograms
=========

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

    
    import gosling as gos

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

        arms = gos.Track(data).mark_rect().encode(
            color=gos.Color("Stain:N",
                domain=["gneg", "gpos25", "gpos50", "gpos75", "gpos100", "gvar"],
                range=["white", "#D9D9D9", "#979797", "#636363", "black", "#A0A0F2"],
            ),
            x=gos.X("chromStart:G", axis="none"),
            xe="chromEnd:G",
            stroke=gos.value("black"),
            strokeWidth=gos.value(0.5),
        ).transform_filter_not("Stain", oneOf=["acen"])

        arm_labels = arms.mark_text().encode(
            text="Name:N",
            color=gos.Color("Stain:N",
                domain=["gneg", "gpos25", "gpos50", "gpos75", "gpos100", "gvar"],
                range=["black", "#636363", "black", "#D9D9D9", "white", "black"],
            ),
            strokeWidth=gos.value(0)
        ).visibility_lt(
            target='mark',
            measure='width',
            threshold='|xe-x|',
            transitionPadding=10
        )

        centromere_base = gos.Track(data).encode(
            x=gos.X("chromStart:G"),
            xe="chromEnd:G",
            color=gos.value('red'),
        ).transform_filter(
            "Stain", oneOf=["acen"]
        )

        centromere_1 = centromere_base.mark_triangleLeft().transform_filter(
            "Name", include="p"
        )

        centromere_2 = centromere_base.mark_triangleRight().transform_filter(
            "Name", include="q"
        )

        ideogram = gos.overlay(arms, arm_labels, centromere_1, centromere_2).properties(width=width, height=20)

        """
        Stacked Bar Charts
        """
        mvdata = gos.multivec(
            url="https://server.gosling-lang.org/api/v1/tileset_info/?d=cistrome-multivec",
            row="sample",
            column="position",
            value="peak",
            categories=["sample 1", "sample 2"],
            binSize=2,
        )

        bar = gos.Track(mvdata).mark_bar().encode(
            x="start:G",
            xe="end:G",
            y="peak:Q",
            color=gos.Color("sample:N"),
        ).properties(width=width, height=20)

        return gos.stack(bar, ideogram).properties(
            xDomain=gos.GenomicDomain(chromosome=chromosome),
            spacing=0
        )

    """
    Composition
    """
    gos.parallel(
        ideogram_with_bars("chr1", 1000),
        ideogram_with_bars("chr2", 970),
        ideogram_with_bars("chr3", 800),
        ideogram_with_bars("chr4", 770),
        ideogram_with_bars("chr5", 740)
    ).properties(
        static=True
    )