insitupy.plotting.cell_abundance_along_axis

insitupy.plotting.cell_abundance_along_axis#

insitupy.plotting.cell_abundance_along_axis(adata, axis, groupby=None, xlim=(0, inf), savepath=None, figsize=(8, 6), save_only=False, dpi_save=300, multiple='stack', histplot_element='bars', kde=False, verbose=True)#

Plot cell abundance along a specified axis.

This function visualizes the distribution of cells along a continuous variable (e.g., pseudotime, spatial coordinate) using histograms or KDE plots. It supports grouping by a categorical variable and allows customization of the histogram style.

Parameters:

  • adata (AnnData) – AnnData object containing single-cell data.

  • axis (Union[str, Tuple[str, str]]) – Key for the x-axis. Can be a column in adata.obs or a tuple (obsm_key, obsm_col) for accessing values from adata.obsm.

  • groupby (Optional[str] (default: None)) – Column in adata.obs to group cells by. Defaults to None.

  • xlim (Tuple (default: (0, inf))) – Range of x-axis values to include. Defaults to (0, np.inf).

  • savepath (Optional[PathLike] (default: None)) – Path to save the figure. If None, the figure is not saved.

  • figsize (Tuple (default: (8, 6))) – Size of the figure in inches. Defaults to (8, 6).

  • save_only (bool (default: False)) – If True, saves the figure without displaying it. Defaults to False.

  • dpi_save (int (default: 300)) – Resolution (DPI) for saving the figure. Defaults to 300.

  • multiple (Literal['layer', 'dodge', 'stack', 'fill'] (default: 'stack')) – How to display multiple groups. Defaults to “stack”.

  • histplot_element (Literal['bars', 'step', 'poly'] (default: 'bars')) – Style of histogram elements. Defaults to “bars”.

  • kde (bool (default: False)) – If True, plots KDE instead of histogram. Defaults to False.

  • verbose (bool (default: True)) – If True, prints progress messages. Defaults to True.

Returns:

Displays and/or saves the generated plot.

Return type:

None