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

.. _gallery_covid:

SARS-CoV-2
==========

Data Source: WashU Virus Genome Browser, NCBI, GISAID

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

    
    import gosling as gos

    gene_data = gos.csv(
        url="https://s3.amazonaws.com/gosling-lang.org/data/COVID/NC_045512.2-Genes.csv",
        chromosomeField="Accession",
        genomicFields=["Start", "Stop"],
    )

    genes_base = gos.Track(gene_data).encode(
        x=gos.X("Start:G"),
        xe=gos.Xe("Stop:G"),
    ).properties(
        width=800,
        height=30,
    )


    genes = gos.overlay(
        genes_base.mark_rect().encode(
            color=gos.value("#0072B2"),
            stroke=gos.value("white"),
            strokeWidth=gos.value(2),
        ),
        genes_base.mark_rule(linePattern=dict(type="triangleRight", size=10)).encode(
            color=gos.value("white"),
            opacity=gos.value(0.6),
            strokeWidth=gos.value(0),
        ),
        genes_base.mark_text().encode(
            text=gos.Text("Gene symbol:N"),
            color=gos.value("black"),
            stroke=gos.value("white"),
            strokeWidth=gos.value(3),
        ).visibility_le(
            target="mark",
            measure="width",
            threshold="|xe-x|",
            transitionPadding=30,
        ),
    ).properties(
        title="NC_045512.2 Genes",
    )

    protein_data = gos.csv(
        url="https://s3.amazonaws.com/gosling-lang.org/data/COVID/sars-cov-2_Sprot_annot_sorted.bed",
        chromosomeField="Accession",
        genomicFields=["Start", "Stop"],
    )

    domain = [
        "receptor-binding domain (RBD)",
        "receptor-binding motif (RBM)",
        "S1/S2 cleavage site",
        "heptad repeat 1 (HR1)",
        "heptad repeat 2 (HR2)",
    ]

    proteins_base = gos.Track(protein_data).encode(
        x=gos.X("Start:G"),
        row=gos.Row("Protein:N", domain=domain),
    ).properties(
        width=800,
        height=80,
    )

    proteins = gos.overlay(
        proteins_base.mark_rect().encode(
            color=gos.Color("Protein:N", domain=domain),
            xe=gos.Xe("Stop:G"),
        ),
        proteins_base.mark_text(textAnchor="end").encode(
            text=gos.Text("Protein:N"),
            color=gos.value("#333"),
            stroke=gos.value("white"),
            strokeWidth=gos.value(3),
        ),
    ).properties(
        title="S Protein Annotation",
    )

    recomb_data = gos.csv(
        url="https://s3.amazonaws.com/gosling-lang.org/data/COVID/TRS-L-dependent_recombinationEvents_sorted.bed",
        chromosomeField="Accession",
        genomicFields=["Start1", "Stop1", "Start2", "Stop2"],
        sampleLength=100,
    )

    recomb = gos.Track(recomb_data).mark_withinLink().encode(
        x=gos.X("Start1:G"),
        xe=gos.Xe("Stop1:G"),
        x1=gos.X1("Start2:G"),
        x1e=gos.X1e("Stop2:G"),
        stroke=gos.value("#0072B2"),
        color=gos.value("#0072B2"),
        opacity=gos.value(0.1),
    ).properties(
        title="TRS-L-Dependent Recombination Events",
        width=800,
        height=400,
    )

    gos.stack(genes, proteins, recomb).properties(
        assembly=[["NC_045512.2", 29903]],
        xDomain=gos.DomainInterval([1, 29903]),
    )