spapros.se.ProbesetSelector.plot_explore_constraint

ProbesetSelector.plot_explore_constraint(selection_method='pca_selection', selection_params=None, background_key='highly_variable', x_axis_key='quantile_0.99', penalty_kernels=None, factors=None, upper=1, lower=0, **kwargs)

Plot histogram of quantiles for selected genes for different penalty kernels.

Parameters:

  • selection_method (str) –

    Selection method to explore. Available are:

    • ”pca_selection”

    • ”DE_selection”

    • ”marker”

  • selection_params (Optional[dict]) – Hyperparameter for the respective gene selection.

  • background_key (str) – Key of column in adata.var containing the values to be plottet as background.

  • x_axis_key (str) – Key of column in adata.var containing the values to be plottet.

  • penalty_kernels (Optional[List[Callable]]) – Any penalty kernel. If None, plateau_penalty_kernel() is used to create three gaussian plateau penalty kernels with different variances. Only then, factors,, lower and upper are used.

  • factors (Optional[List[float]]) – Factors for the variance for creating a gaussian penalty kernel.

  • lower (float) – Lower border above which the kernel is 1.

  • upper (float) – Upper boder below which the kernel is 1.

  • **kwargs – Further arguments for explore_constraint().

Returns:

Figure can be shown (default True) and stored to path (default None). Change this with show and save in kwargs.