cellfish.plot.plot1cell

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cellfish.plot.plot1cell#

cellfish.plot.plot1cell(adata, clusters, basis='X_umap', tracks=None, *, coord_scale=0.8, point_size=3.0, point_alpha=0.3, contour_levels=(0.2, 0.3), contour_color='#ae9c76', kde_n=200, do_label=True, label_fontsize=9.0, label_orient='radial', cluster_palette=None, track_palette=None, track_palettes=None, bg_color=None, gap_between_deg=2.0, gap_start_deg=12.0, cluster_track_width=0.035, track_width=0.025, track_gap=0.004, cluster_label_pad=0.03, show_ticks=True, tick_fontsize=4.5, tick_length=0.012, figsize=(7, 7), ax=None, show=True, return_data=False)#

Circular UMAP with metadata tracks.

Mirrors plot1cell::plot_circlize (Wu 2021). Clusters are laid out as arc sectors on the circumference, sector length proportional to log10(n_cells). The scatter is drawn in Cartesian coordinates inside the unit circle, with a Gaussian-KDE contour overlay. Each entry in tracks becomes one extra concentric ring coloured by the run-length segments of that metadata column within each cluster sector.

Parameters:

  • adata (AnnData)

  • clusters (str) – Key in adata.obs giving the cluster label per cell.

  • basis (str) – Key in adata.obsm; first two columns are used.

  • tracks (list[str] | None) – Additional adata.obs columns to show as outer rings.

  • coord_scale (float) – zoom parameter from the R version; the scatter fills [-coord_scale, coord_scale] on each axis.

  • contour_levels (tuple[float, ...] | None) – Level set(s) of the 2-D KDE to overlay. None disables contours.

  • gap_between_deg (float) – Angular gaps (degrees) between adjacent cluster sectors and at the circle’s starting point.

  • gap_start_deg (float) – Angular gaps (degrees) between adjacent cluster sectors and at the circle’s starting point.

  • cluster_track_width (float) – Radial thickness of the cluster ring and each metadata ring, expressed as a fraction of the unit radius.

  • track_width (float) – Radial thickness of the cluster ring and each metadata ring, expressed as a fraction of the unit radius.

  • ax (matplotlib Axes | None) – If given, draw into it (must be aspect='equal'). A new figure is created otherwise.

  • return_data (bool) – If True, also return the per-cell dataframe used for plotting (useful for reproducing or extending the figure).

  • point_size (float)

  • point_alpha (float)

  • contour_color (str)

  • kde_n (int)

  • do_label (bool)

  • label_fontsize (float)

  • label_orient (str)

  • track_palettes (Sequence | None)

  • bg_color (str | None)

  • track_gap (float)

  • cluster_label_pad (float)

  • show_ticks (bool)

  • tick_fontsize (float)

  • tick_length (float)

  • show (bool)

Returns:

-ax (Axes) (ax, df) if return_data=True.

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