stereo.plots.ClustersGenesScatter.clusters_genes_scatter

ClustersGenesScatter.clusters_genes_scatter(cluster_res_key, dendrogram_res_key=None, topn=5, gene_names=None, expression_kind='mean', groups=None, width=None, height=None, colormap='Reds', standard_scale='gene')[source]

Scatter representing mean expression of genes on each cell cluster.

Parameters:

  • cluster_res_key (str) – the key to get cluster result.

  • dendrogram_res_key (Optional[str]) – the key to get dendrogram result, defaults to None to avoid show dendrogram on plot.

  • topn (Optional[int]) – select topn expressed genes in each cluster, defaults to 5, ignored if gene_names is not None, the number of genes shown in plot may be more than topn because the topn genes in each cluster are not the same.

  • gene_names (Optional[Sequence[str]]) – a list of genes to show, defaults to None to show all genes.

  • expression_kind (Literal['mean', 'sum']) – the kind of expression to show, ‘mean’ or ‘sum’, defaults to ‘mean’.

  • groups (Optional[Sequence[str]]) – a list of cell clusters to show, defaults to None to show all cell clusters.

  • width (Optional[int]) – the figure width in pixels, defaults to None

  • height (Optional[int]) – the figure height in pixels, defaults to None

  • colormap (str) – colormap used on plot, defaults to ‘Reds’

  • standard_scale (str) – Whether or not to standardize that dimension between 0 and 1, meaning for each gene or cluster, subtract the minimum and divide each by its maximum, defaults to ‘gene’