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], optional) – Column in adata.obs to group cells by. Defaults to None.

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

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

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

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

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

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

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

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

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

Returns:

Displays and/or saves the generated plot.

Return type:

None

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