cellfish.plot.add_contour

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cellfish.plot.add_contour#

cellfish.plot.add_contour(ax, adata, groupby, clusters, basis='X_umap', grid_density=100, contour_threshold=0.1, **kwargs)#

Add density contour to plot.

Parameters:

  • ax (matplotlib.axes.Axes) – Axis to plot on.

  • adata (AnnData) – AnnData object.

  • groupby (str) – Column to group by.

  • clusters (List[str]) – Clusters to plot.

  • basis (str, optional) – Embedding key in adata.obsm.

  • grid_density (int, optional) – Grid density for KDE.

  • contour_threshold (float, optional) – Threshold for contour levels.

  • **kwargs – Additional arguments for ax.contour.

Returns:

matplotlib.axes.Axes Axis with contour added.

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