sparrow.pl.cluster

sparrow.pl.cluster(sdata, table_layer, key_added='leiden', output=None)

Visualize clusters.

Plot sthe clusters on a UMAP (using scanpy.pl.umap), and shows the most differentially expressed genes/channels for each cluster on a second plot (using scanpy.pl.rank_genes_group), if “rank_genes_groups” is in sdata.tables[table_layer].uns.keys().

Parameters:

• sdata (SpatialData) – The SpatialData object containing the analyzed data.

• table_layer (str) – The table layer in sdata to visualize.

• key_added (str (default: 'leiden')) – name of the column in sdata.tables[table_layer].obs that contains the cluster id.

• output (Optional[str] (default: None)) – The file path prefix for the plots (default is None). If provided, the plots will be saved to the specified output file path with “_umap.png” and “_rank_genes_groups.png” as suffixes. If None, the plots will be displayed directly without saving.

Return type:

None

Returns:

: None

See also

sparrow.tb.leiden, sparrow.tb.kmeans