cellcharter.pl.shape_metrics

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cellcharter.pl.shape_metrics#

cellcharter.pl.shape_metrics(adata, condition_key, condition_groups=None, cluster_key=None, cluster_id=None, component_key='component', metrics=('linearity', 'curl'), fontsize='small', figsize=(8, 7), title=None)#

Boxplots of the shape metrics between two conditions.

Parameters:

  • adata (AnnData) – Annotated data object.

  • condition_key (str) – Key in anndata.AnnData.obs where the condition labels are stored.

  • condition_groups (Optional[list[str]] (default: None)) – List of two conditions to compare. If None, all pairwise comparisons are made.

  • cluster_key (Optional[str] (default: None)) – Key in anndata.AnnData.obs where the cluster labels are stored. This is used to filter the clusters to plot.

  • cluster_id (Optional[list[str]] (default: None)) – List of clusters to plot. If None, all clusters are plotted.

  • component_key (str (default: 'component')) – Key in anndata.AnnData.obs where the component labels are stored.

  • metrics (str | tuple[str] | list[str] (default: ('linearity', 'curl'))) – List of metrics to plot. Available metrics are linearity, curl, elongation, purity.

  • figsize (tuple[float, float] (default: (8, 7))) – Figure size.

  • title (Optional[str] (default: None)) – Title of the plot.

Return type:

None

Returns:

Nothing, just plots the figure and optionally saves the plot.

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