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

.. _gallery_comparative_matrices:

Comparative Matrices
====================

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

    
    import gosling as gos

    size = 375
    scaled_size = size / 15

    # Data

    HFFc6_H3K4me3 = gos.bigwig(
        url="https://s3.amazonaws.com/gosling-lang.org/data/HFFc6_H3K4me3.bigWig",
        column="position",
        value="peak",
        binSize=8,
    )

    HFFc6_Atacseq = gos.bigwig(
        url="https://s3.amazonaws.com/gosling-lang.org/data/HFFc6_Atacseq.mRp.clN.bigWig",
        column="position",
        value="peak",
        binSize=8
    )

    HFFC6_CTCF = gos.bigwig(
        url="https://s3.amazonaws.com/gosling-lang.org/data/HFFC6_CTCF.mRp.clN.bigWig",
        column="position",
        value="peak",
        binSize=8,
    )

    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"},
        ],
    )

    micro_c = gos.matrix("https://server.gosling-lang.org/api/v1/tileset_info/?d=hffc6-microc-hg38")
    hi_c = gos.matrix("https://server.gosling-lang.org/api/v1/tileset_info/?d=hffc6-hic-hg38")

    epilogos_data = gos.multivec(
        url="https://server.gosling-lang.org/api/v1/tileset_info/?d=epilogos-hg38",
        row="category",
        column="position",
        value="value",
        categories=[
            "Active TSS", "Flanking Active TSS", "Transcr at gene 5\\' and 3\\'",
            "Strong transcription", "Weak transcription", "Genic enhancers",
            "Enhancers", "ZNF genes & repeats", "Heterochromatin",
            "Bivalent/Poised TSS", "Flanking Bivalent TSS/Enh", "Bivalent Enhancer",
            "Repressed PolyComb", "Weak Repressed PolyComb", "Quiescent/Low",
        ],
        binSize=8,
    )

    # Tracks & Views

    track1 = gos.Track(HFFc6_H3K4me3).mark_bar().encode(
        x=gos.X("start:G", axis="top"),
        xe="end:G",
        y=gos.Y("peak:Q", axis="none"),
        color=gos.value("darkgreen"),
    ).properties(title="HFFc6_H3K4me3", height=size, width=scaled_size)

    track2 = gos.Track(HFFc6_Atacseq).mark_bar().encode(
        x="start:G",
        xe="end:G",
        y=gos.Y("peak:Q", axis="none"),
        color=gos.value("#E79F00"),
    ).properties(title="HFFc6_ATAC", height=size, width=scaled_size)

    gene_anno_base = gos.Track(genes).encode(
        x="start:G",
        size=gos.value(13),
        stroke=gos.value("white"),
        strokeWidth=gos.value(1),
        color=gos.value("#CB7AA7"),
        row=gos.Row("strand:N", domain=["+", "-"]),
    )

    gene_overlay = gos.overlay(
        gos.Track(HFFC6_CTCF).mark_bar().encode(
            x="start:G",
            xe="end:G",
            y=gos.Y("peak:Q", axis="none"),
            color=gos.value("#0072B2")
        ),
        gene_anno_base.mark_triangleRight(backgroundOpacity=0).encode(
            color=gos.value("#CB7AA7"),
        ).transform_filter("strand", oneOf=["+"]),
        gene_anno_base.mark_triangleLeft(backgroundOpacity=0).encode(
            color=gos.value("#029F73"),
        ).transform_filter("strand", oneOf=["-"]).properties(title="HFFC6_CTCF")
    ).properties(height=size, width=scaled_size)

    # Configure Layout

    left = gos.stack(track1, track2, gene_overlay).properties(
        orientation="vertical",
        yOffset=size / 2.78,
    )

    top = gos.stack(
        track1.properties(width=size, height=scaled_size),
        track2.properties(width=size, height=scaled_size),
        gene_overlay.properties(width=size, height=scaled_size),
    )

    matrix = gos.Track(micro_c).mark_rect().encode(
        x="xs:G",
        xe="xe:G",
        y="ys:G",
        ye="ye:G",
        color=gos.Color("value:Q", range="warm"),
    ).properties(title="HFFc6_Micro-C", width=size, height=size)


    bottom = gos.Track(epilogos_data).mark_bar().encode(
        x=gos.X("start:G", axis="none"),
        xe="end:G",
        y=gos.Y("value:Q", axis="none"),
        color=gos.Color("category:N", range=[
            "#FF0000", "#FF4500", "#32CD32", "#008000", "#006400",
            "#C2E105", "#FFFF00", "#66CDAA", "#8A91D0", "#CD5C5C",
            "#E9967A", "#BDB76B", "#808080", "#C0C0C0", "gray"
        ]),
    ).transform_filter("value", inRange=[0, 999999]).properties(
        title="Epilogos (hg38)",
        width=size,
        height=scaled_size,
    )


    left_matrix = gos.vertical(top, matrix, bottom, spacing=0)
    right_matrix = gos.vertical(
        top,
        # replace data source for right side, change title
        matrix.properties(data=hi_c, title="HFFc6_Hi-C"),
        bottom,
        spacing=0,
    )

    right = gos.View(views=[left_matrix, right_matrix], spacing=30)

    gos.horizontal(left, right).properties(
        title="Matrix Visualization",
        subtitle="Comparison of Micro-C and Hi-C for HFFc6 Cells",
        xDomain=gos.GenomicDomain(chromosome="chr7", interval=[77700000, 81000000]),
        spacing=1,
        linkingId="-"
    )