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)#

Plot cell abundance along a specified observation value.

Parameters:

  • adata (AnnData) – Annotated data matrix.

  • axis (Union[str, Tuple[str, str]]) – Observation category to be plotted on the x-axis. Can be a string representing a column in adata.obs or a tuple (obsm_key, obsm_col) where obsm_key is a key in adata.obsm and obsm_col is a column in the corresponding DataFrame.

  • groupby (Optional[str], optional) – Column in adata.obs to group by. Defaults to None.

  • xmin (Number, optional) – Minimum value of obs_val to include in the plot. Defaults to 0.

  • savepath (Optional[os.PathLike], optional) – Path to save the figure. Defaults to None.

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

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

  • dpi_save (int, optional) – Dots per inch for saving the figure. Defaults to 300.

  • histplot_multiple (str, optional) – How to plot multiple histograms. Options are “layer”, “dodge”, “stack”, “fill”. Defaults to “stack”.

  • histplot_element (str, optional) – Plotting element. Options are “bars”, “step”, “poly”. Defaults to “bars”.

Returns:

None

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