enrichmap.pl.spatial_enrichmap

enrichmap.pl.spatial_enrichmap#

enrichmap.pl.spatial_enrichmap()#

Visualise spatial enrichment maps for given signatures using spatial scatter plots.

Parameters:

  • adata (AnnData) – Annotated data matrix containing spatial and gene expression information.

  • score_key (str or list of str, optional) – A list of signature names for which enrichment scores are plotted. Defaults to [“enrichmap_score”].

  • cmap (str, optional) – Colormap for visualisation. Defaults to “RdBu_r”.

  • library_key (str or None, optional) – Key in adata.obs for library identifiers. Defaults to “library_id”.

  • library_id (str or list of str, optional) – Specific library ID(s) to visualise. Defaults to all libraries.

  • img_alpha (float, optional) – Alpha value for image overlay. Defaults to 0.5.

  • ncols (int, optional) – Number of columns in the grid layout. Defaults to length of score_key.

  • size (int, optional) – Scatter plot marker size. Defaults to 1.5.

  • vcenter (int, optional) – Central value for colour scaling. Defaults to 0.

  • save (str or None, optional) – Filename to save the plot. If None, plot is not saved.

  • **kwargs (dict, optional) – Additional arguments passed to sq.pl.spatial_scatter.

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