cellcharter.pl.enrichment

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cellcharter.pl.enrichment#

cellcharter.pl.enrichment(adata, group_key, label_key, dot_scale=3, group_cluster=True, label_cluster=False, groups=None, labels=None, show_pvalues=False, significance=None, enriched_only=True, significant_only=False, size_threshold=None, palette=None, fontsize='small', figsize=(7, 5), save=None, **kwargs)#

Plot a dotplot of the enrichment of label_key in group_key.

Parameters:

  • adata (AnnData) – Annotated data object.

  • group_key (str) – Key in anndata.AnnData.obs where groups are stored.

  • label_key (str) – Key in anndata.AnnData.obs where labels are stored.

  • dot_scale (float (default: 3)) – Scale of the dots.

  • group_cluster (bool (default: True)) – If True, display groups ordered according to hierarchical clustering.

  • label_cluster (bool (default: False)) – If True, display labels ordered according to hierarchical clustering.

  • groups (Optional[list] (default: None)) – The groups for which to show the enrichment.

  • labels (Optional[list] (default: None)) – The labels for which to show the enrichment.

  • show_pvalues (bool (default: False)) – If True, show p-values as colors.

  • significance (Optional[float] (default: None)) – If not None, show fold changes with a p-value above this threshold in a lighter color.

  • enriched_only (bool (default: True)) – If True, display only enriched values and hide depleted values.

  • significant_only (bool (default: False)) – If True, display only significant values and hide non-significant values.

  • size_threshold (Optional[float] (default: None)) – Threshold for the size of the dots. Enrichment or depletions with absolute value above this threshold will have all the same size.

  • palette (Union[str, ListedColormap, None] (default: None)) – Colormap for the enrichment values. It must be a diverging colormap.

  • figsize (tuple[float, float] | None (default: (7, 5))) – Size of the figure in inches.

  • dpi – Dots per inch.

  • save (Union[str, Path, None] (default: None)) – Whether to save the plot.

  • kwargs – Keyword arguments for matplotlib.pyplot.scatter().

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