omicverse.pl.add_density_contour

omicverse.pl.add_density_contour(ax, embeddings, weights, levels='quantile', n_quantiles=5, bw_adjust=0.3, cmap_contour='Greys', linewidth=1.0, zorder=10, fill=False, alpha=0.4)[source]

Add KDE-based density contours to an existing matplotlib plot.

Parameters:

  • ax – matplotlib.axes.Axes object to draw contours on

  • embeddings – 2D coordinate array with shape (n_cells, 2)

  • weights – 1D weight array for KDE, will be min-max normalized

  • levels (default: 'quantile') – Contour level specification - ‘quantile’ or list of values (‘quantile’)

  • n_quantiles (default: 5) – Number of quantile levels when levels=’quantile’ (5)

  • bw_adjust (default: 0.3) – Bandwidth adjustment factor for KDE (0.3)

  • cmap_contour (default: 'Greys') – Colormap for contour lines (‘Greys’)

  • linewidth (default: 1.0) – Width of contour lines (1.0)

  • zorder (default: 10) – Drawing order for contours (10)

  • fill (default: False) – Whether to fill contours (False for lines, True for filled)

  • alpha (default: 0.4) – Transparency for filled contours (0.4)

Returns:

matplotlib contour object for potential colorbar addition

Return type:

cs