campa.pl.plot_mean_intensity

plot_mean_intensity(adata, groupby='cluster', marker_dict=None, save=None, dendrogram=False, limit_to_groups=None, type='matrixplot', cmap='viridis', adjust_height=True, figsize=(10, 5), ax=None, **kwargs)[source]

Show per cluster intensity of each channel.

Intensity is either shown as mean or z-scored intensity, depending on the standard_scale keyword argument.

Parameters

  • adata (AnnData) – Adata containing aggregated information by clusters. E.g. result of FeatureExtractor.get_intensity_adata().

  • groupby (str) – column in adata.obs containing the groups to compare.

  • marker_dict (Union[Mapping[str, Iterable[str]], Iterable[str], None]) – Limit/group vars that are shown, either by passing list or dict (adds annotations to plot).

  • save (Optional[str]) – Path to save figure to.

  • dendrogram (bool) – Show dendrogram over columns.

  • limit_to_groups (Optional[Mapping[str, Union[str, List[str]]]]) – Dict with obs as keys and groups from obs as values, to subset adata before plotting.

  • type (str) – Type of plot, either matrixplot or violinplot.

  • cmap (str) – Matplotlib colormap to use.

  • adjust_height (bool) – Option to make plots a bit more streamlined.

  • figsize (Tuple[int, int]) – Size of figure.

  • ax (Optional[Axes]) – Axis to plot in.

  • kwargs (Any) – Keyword arguments for sc.pl.stacked_violin()/sc.pl.matrixplot().

Return type

None