bioalpha.singlecell.plotting.aucell_heatmap

bioalpha.singlecell.plotting.aucell_heatmap(adata: AnnData, gene_sets: Sequence[str] | None = None, groupby: str = 'index', groups: Literal['all'] | Sequence[str] | slice = 'all', key: str = 'aucell', dendorgram: bool = True, show: bool = True, save: bool = False, **kwds)

Plotting AUC scores of cells and gene_sets.

Parameters:

  • adata (AnnData) – The annotated data matrix of shape n_obs x n_vars. Rows correspond to cells and columns to genes.

  • gene_sets (Optional[Sequence[str]], default = None) – Name of gene sets to plot.

  • groupby (str, default = "index") – The key of the observations grouping to consider.

  • groups (Union[Literal["all"], Sequence[str]], default = "all") – The groups for which to show the cells scores. If groups is None, set it to all cells.

  • key (str, default = "aucell") – Key used to plot the AUC score that stored in adata.obsm.

  • dendorgram (bool, default = True) – If True, a dendrogram based on the hierarchical clustering between the groupby categories is added.

  • show (Optional[bool], default = True) – Show the plot, do not return axis.

  • save (Optional[bool], default = False) – If True, save the figure.

  • kwds (dict) – Keyword arguments passed to seaborn.clustermap.