insitupy.plotting.cell_expression_along_axis

insitupy.plotting.cell_expression_along_axis#

insitupy.plotting.cell_expression_along_axis(adata, axis, genes, cell_type_column, cell_type, xlim=(0, inf), min_expression=0, xlabel=None, fit_reg=False, kde=False, maxcols=4, savepath=None, save_only=False, dpi_save=300, fig_height=4, fig_marginal_ratio=0.15, scatter_size=1, wspace=0.15, hspace=0.25, font_scale_factor=1)#

Plot gene expression along a specified axis for a given cell type.

Parameters:

  • adata – AnnData object containing the single-cell data.

  • axis – Observation value to plot along the x-axis.

  • genes (List[str]) – List of genes to plot.

  • cell_type_column – Column name in adata.obs that contains cell type information.

  • cell_type – Specific cell type to filter the data.

  • xlim (Tuple[Union[int, float], Union[int, float]], optional) – Limits for the x-axis. Defaults to (0, np.inf).

  • min_expression (Union[int, float], optional) – Minimum expression level to include in the plot. Defaults to 0.

  • xlabel (Optional[str], optional) – Label for the x-axis. Defaults to None.

  • fit_reg (bool, optional) – Whether to fit a regression line. Defaults to False.

  • lowess (bool, optional) – Whether to use LOWESS for regression. Defaults to False.

  • robust (bool, optional) – Whether to use a robust regression. Defaults to False.

  • fig_height (Number, optional) – Height of the figure. Defaults to 4.

  • fig_marginal_ratio (Number, optional) – Ratio of the marginal plot height to the main plot height. Defaults to 0.2.

  • scatter_size (Number, optional) – Size of the scatter plot points. Defaults to 1.

Returns:

Displays the plot.

Return type:

None

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