snapatac2.pl.umap#

snapatac2.pl.umap(adata, color, use_rep='X_umap', marker_size=2, marker_opacity=0.5, width=550, height=500, show=True, interactive=True, out_file=None)[source]#

Plot the UMAP embedding.

Parameters

  • adata (AnnData) – Annotated data matrix.

  • color (str | np.ndarray) – If the input is a string, it will be used the key to retrieve values from obs.

  • use_rep (str) – Use the indicated representation in .obsm.

  • marker_size (float) – Size of the dots.

  • marker_opacity (float) – Opacity of the dots.

  • width (float) – The width of the plot.

  • height (float) – The height of the plot.

  • interactive (bool) – Whether to make interactive plot.

  • out_file (str | None) – Path of the output file for saving the output image, end with ‘.svg’ or ‘.pdf’ or ‘.png’ or ‘.html’.

Returns

If show=False and out_file=None, an plotly.graph_objects.Figure will be returned, which can then be further customized using the plotly API.

Return type

‘plotly.graph_objects.Figure’ | None