Add dark-background 3D UMAP rotation for profile

Author: Ekin-Kahraman

docs/slow_rotation.gif

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+"""Slow-rotating 3D UMAP for profile banner. Clean, minimal, floaty."""
+
+import scanpy as sc
+import matplotlib.pyplot as plt
+import imageio.v3 as iio
+from pathlib import Path
+from io import BytesIO
+
+RESULTS_DIR = Path("results")
+
+PALETTE = {
+    "CD4+ T cells": "#E69F00",
+    "CD8+ T cells": "#56B4E9",
+    "NK cells": "#009E73",
+    "B cells": "#F0E442",
+    "CD14+ Monocytes": "#0072B2",
+    "FCGR3A+ Monocytes": "#D55E00",
+    "Dendritic cells": "#CC79A7",
+    "Megakaryocytes": "#999999",
+}
+
+BG = "#0d1117"
+N_FRAMES = 120
+FPS = 20
+
+
+def render_frame(coords_3d, cell_types, azim, elev=20):
+    fig = plt.figure(figsize=(9, 6), facecolor=BG)
+    ax = fig.add_subplot(111, projection="3d", facecolor=BG)
+
+    for ct in cell_types.cat.categories:
+        mask = cell_types == ct
+        ax.scatter(
+            coords_3d[mask, 0], coords_3d[mask, 1], coords_3d[mask, 2],
+            c=PALETTE.get(ct, "#AAAAAA"), s=5, alpha=0.8,
+            label=ct, edgecolors="none",
+        )
+
+    ax.view_init(elev=elev, azim=azim)
+
+    # Clean axes
+    ax.set_xticks([])
+    ax.set_yticks([])
+    ax.set_zticks([])
+    ax.xaxis.pane.fill = False
+    ax.yaxis.pane.fill = False
+    ax.zaxis.pane.fill = False
+    ax.xaxis.pane.set_edgecolor(BG)
+    ax.yaxis.pane.set_edgecolor(BG)
+    ax.zaxis.pane.set_edgecolor(BG)
+    ax.xaxis.line.set_color(BG)
+    ax.yaxis.line.set_color(BG)
+    ax.zaxis.line.set_color(BG)
+    ax.grid(False)
+
+    ax.legend(
+        loc="upper left", fontsize=7, framealpha=0.0,
+        labelcolor="#c9d1d9", edgecolor="none",
+        markerscale=3,
+    )
+
+    fig.subplots_adjust(left=0, right=1, top=1, bottom=0)
+    buf = BytesIO()
+    fig.savefig(buf, format="png", dpi=110, facecolor=BG, edgecolor="none")
+    plt.close(fig)
+    buf.seek(0)
+    return iio.imread(buf)
+
+
+def main():
+    adata = sc.read_h5ad(RESULTS_DIR / "05_annotated.h5ad")
+    print(f"Loaded {adata.n_obs} cells")
+
+    # Compute 3D UMAP
+    if "neighbors" not in adata.uns:
+        sc.pp.neighbors(adata, n_neighbors=15, n_pcs=40)
+    sc.tl.umap(adata, n_components=3)
+    coords_3d = adata.obsm["X_umap"]
+    cell_types = adata.obs["cell_type"]
+
+    print(f"Rendering {N_FRAMES} frames...")
+    frames = []
+    for i in range(N_FRAMES):
+        azim = (i / N_FRAMES) * 360
+        frame = render_frame(coords_3d, cell_types, azim)
+        frames.append(frame)
+        if (i + 1) % 30 == 0:
+            print(f"  {i + 1}/{N_FRAMES}")
+
+    out_path = Path("docs") / "slow_rotation.gif"
+    out_path.parent.mkdir(exist_ok=True)
+    iio.imwrite(out_path, frames, duration=int(1000 / FPS), loop=0)
+    print(f"Done! {out_path.stat().st_size / 1024 / 1024:.1f} MB")
+
+
+if __name__ == "__main__":
+    main()