PBMC UMAP

Explore cell types in a zoomable single-cell embedding.

Each dot is a cell, colored by cell type. Use the mouse wheel to zoom and drag to pan. Hover over a dot to identify the cell and its type.

Compare where genes are expressed in the UMAP panels.

Data use and provenance

2,638 cells from Scanpy’s processed 10x Genomics PBMC3k dataset (CC BY 4.0), retaining its saved UMAP coordinates, log-transformed counts, and cell-type labels.

Inspired by Scanpy’s UMAP examples.

Code

"""PBMC UMAP.

Explore cell types in a zoomable single-cell embedding.
"""

import genome_spy as gs
from genome_spy.anndata import from_anndata
from genome_spy.datasets import _load_table_bundle as load_data
from genome_spy.datasets._pbmc import pbmc_markers


adata = pbmc_markers()
data = load_data("pbmc_markers", ("groups",))
cells = from_anndata(
    adata, obs=["cell", "cell_type"], obsm_keys=[("X_umap", 0), ("X_umap", 1)]
)
colors = gs.Scale(
    domain=data["groups"]["cell_type"].tolist(),
    range=data["groups"]["color"].tolist(),
)
zoom = gs.Expression("zoomLevel")
chart = (
    gs.Chart(cells)
    .mark_point(
        size=gs.expr(gs.expr.min(18 * gs.expr.pow(zoom, 0.6), 90)), opacity=0.85
    )
    .encode(
        x=gs.X("X_umap-0:Q")
        .scale(
            name="pbmc-umap-x",
            domain=data["umap_domains"]["x"],
            zero=False,
            nice=False,
            zoom=True,
        )
        .axis(title="UMAP 1", labels=False, ticks=False, domain=False, grid=False),
        y=gs.Y("X_umap-1:Q")
        .scale(
            name="pbmc-umap-y",
            domain=data["umap_domains"]["y"],
            zero=False,
            nice=False,
            zoom=True,
        )
        .axis(title="UMAP 2", labels=False, ticks=False, domain=False, grid=False),
        color=gs.Color("cell_type:N")
        .scale(colors)
        .legend(title="Cell type", orient="bottom", columns=4),
        tooltip=["cell:N", "cell_type:N"],
    )
    .properties(height=520, title="PBMC cell types")
)

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