moscot.plotting.cell_transition

moscot.plotting.cell_transition(obj, key='cell_transition', row_label=None, col_label=None, annotate='{x:.2f}', fontsize=7.0, cmap='viridis', cbar_kwargs=mappingproxy({}), ax=None, return_fig=False, figsize=None, dpi=None, save=None, **kwargs)

Plot an aggregate cell transition matrix.

See also

• See Cell transitions on how to compute and plot the cell transitions.

Parameters:

• obj (Union[AnnData, Tuple[AnnData, AnnData], CompoundProblem]) –

  Object containing the cell transition data. Valid options are:

  • AnnData - annotated data object containing the data.

  • tuple - source and target AnnData objects.

  • CompoundProblem - one of the moscot.problems.

• key (str) – Key in uns['moscot_results'] where the cell transition data is stored.

• row_label (Optional[str]) – Label for the rows of the transition matrix.

• col_label (Optional[str]) – Label for the columns of the transition matrix.

• annotate (Optional[str]) – Format used when annotating the cells. If None, don’t annotate the cells.

• fontsize (float) – Font size for the annotations.

• cmap (Union[str, Colormap]) – Colormap of the heatmap.

• cbar_kwargs (Mapping[str, Any]) – Keyword arguments for colorbar().

• ax (Optional[Axes]) – Ax used for plotting. If None, create a new one.

• return_fig (bool) – Whether to return the figure.

• figsize (Optional[Tuple[float, float]]) – Size of the figure.

• dpi (Optional[int]) – Dots per inch.

• save (Union[str, Path, None]) – Path where to save the figure.

• kwargs (Any) – Keyword arguments for text().

Return type:

Figure

Returns:

: If return_fig = True, returns and plots the figure. Otherwise, just plots the figure.