scanpy.external.pl.sam

scanpy.external.pl.sam(adata, projection='X_umap', *, c=None, cmap='Spectral_r', linewidth=0.0, edgecolor='k', axes=None, colorbar=True, s=10.0, **kwargs)

Scatter plot using the SAM projection or another input projection.

Parameters:

projection str | ndarray (default: 'X_umap')

A case-sensitive string indicating the projection to display (a key in adata.obsm) or a 2D numpy array with cell coordinates. If None, projection defaults to UMAP.

c str | ndarray | None (default: None)

Cell color values overlaid on the projection. Can be a string from adata.obs to overlay cluster assignments / annotations or a 1D numpy array.

axes Axes | None (default: None)

Plot output to the specified, existing axes. If None, create new figure window.

kwargs Any

all keyword arguments in matplotlib.pyplot.scatter are eligible.

Return type:

Axes