bioalpha.singlecell.plotting.aucell

bioalpha.singlecell.plotting.aucell(adata: AnnData, gene_sets: Sequence[str] | None = None, key: str = 'aucell', basis: str | None = None, cmap='YlOrRd', **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. Maximum only 12 gene sets.

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

  • basis (Optional[str], default = None) – The embedding to plotting. If None, select X_umap or X_tsne.

  • 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.