singleCellHaystack.plot_gene_clusters

singleCellHaystack.plot_gene_clusters(adata, gene_clusters, basis=None, ncols=None, figsize=None, color_map='coolwarm', return_scores=False)

Plot gene clusters returned by cluster_genes.

Parameters:

• adata – AnnData object.

• gene_clusters – pandas DataFrame output by cluster_genes.

• basis – the embedding to use.

• ncols – numner of columns for plot.

• figsize – the size of the figure.

• color_map – which color map to use.

• return_scores – whether to return the calculated gene scores.