Zoomable t-SNE scatter plot

Explore a dense embedding with sample colors and points that grow on zoom.

Zoom in to explore the dense point cloud. Points grow as you zoom, while colors distinguish the sample groups. Drag to pan around the embedding.

Data use and provenance

This adapts GenomeSpy’s t-SNE example and loads its hosted Parquet file directly. The upstream specification calls this an unsuccessful t-SNE attempt and does not identify the original study or data-specific license. Use it as an interaction demonstration, not evidence of meaningful biological clusters. Loading requires an internet connection; the dataset is not bundled with the Python package.

Code

"""Zoomable t-SNE scatter plot.

Explore a dense embedding with sample colors and points that grow on zoom.
"""

import genome_spy as gs


# Read the upstream Parquet file directly, without copying it into the spec.
data = gs.Data(
    url="https://genomespy.app/examples/tSNE/tsne.parquet",
    format=gs.DataFormat(type="parquet"),
)

# These are live GenomeSpy view values, not Python-side measurements.
zoom = gs.Expression("zoomLevel")
width = gs.Expression("width")
height = gs.Expression("height")

points = (
    gs.Chart()
    .mark_point(
        size=gs.expr(
            gs.expr.min(0.1 * zoom * gs.expr.sqrt(zoom), 200)
            * (width * height / (500 * 500))
        )
    )
    .encode(color=gs.Color("sample:N"), opacity=gs.value(0.7))
)

# Keep the original example's playful notes at their plotted positions.
notes = (
    gs.Chart(
        gs.Data(
            values=[
                {"x": -1.565, "y": 7.41, "text": "Ouch, that's sharp!"},
                {"x": 5.6, "y": -3.7, "text": "What's this pink mass?"},
                {"x": -4.8, "y": -7.1, "text": "An artistic appendage."},
            ]
        )
    )
    .mark_text(dy=12, align="center", size=17, font="Indie Flower", angle=5)
    .encode(text=gs.Text("text:N"))
)

# Both layers use the same zoomable coordinates.
chart = (
    (points + notes)
    # Let the plot fit the gallery container, including its axes and legend.
    .properties(data=data, title="Zoomable t-SNE scatter plot")
    .encode(
        x=gs.X("x:Q").scale(domain=[-10, 10], zoom=True),
        y=gs.Y("y:Q").scale(domain=[-10, 10], zoom=True),
    )
)

Show generated specification