spapros.pl.selection_histogram

spapros.pl.selection_histogram(adata, selections_dict, x_axis_keys, background_key='highly_variable', penalty_kernels=None, penalty_keys=None, penalty_labels='penalty', upper_borders=None, lower_borders=None, size_factor=4.5, legend_size=11, show=True, save=None)

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

Parameters

  • adata (AnnData) – sc.AnnData object containing the data for plotting the histogram in adata.var[x_axis_key].

  • selections_dict (Dict[str, DataFrame]) – Dictionary of dataframes with gene identifiers as index and a boolean column indicating the selection. The dictionary keys are used as label in the plot and need to be equivalent to the keys in penalty_kernels and penalty_keys.

  • x_axis_keys (Dict[str, str]) –

    Dictionary with the column in adata.var that is used for the x axis of the plotted histograms. There are two reasonable options:

    • If a penalty is plottet: the column containing the values of which the penalty scores were derived by applying the penalty kernel. Use the penalty_key as dictionary key in this case.

    • If no penalty is plottet: a column containing some statistic, eg. 99% quantile. Use the same keys as selection_dict in this case.

  • background_key (str) – Key of column in adata.var which is plottet as background histogram. If None, no background histogram is plotted. If ‘all’, all genes are used as background.

  • penalty_kernels (Optional[Dict[str, Dict[str, Callable]]]) – Dictionary of penalty kernels, which were used for each selection. The outer key is the selection name. The inner keys are used as subplot titles. Additionally, penalty_keys can be provided. If both are None, only the histograms are plottet.

  • penalty_keys (Optional[Dict[str, List[str]]]) – Dictionary of a list of column keys of adata.var containing penalty scores for each selection. Additionally, penalty_kernels can be provided. If both are None, only the histograms are plottet.

  • penalty_labels (Union[str, Dict[str, Dict[str, str]]]) – A legeng label for each selection and each penalty. The keys of the outer dictionary need to be the selection names. As keys for the inner dictionary, use the penalty keys.

  • upper_borders (Optional[Union[bool, Dict[str, Union[float, bool]]]]) – Dictionary with the lower borders above which the kernels are 1, which is indicated as a vertical line in the plot. Use the same dictionay keys as penalty_keys or penalty_kernels. If None, it is automatically infered. If False or not in the dictionary, no vertical line at the upper border is drawn.

  • lower_borders (Optional[Union[bool, Dict[str, Union[float, bool]]]]) – Dictionary with the upper borders below which the kernels are 1, which is indicated as a vertical line in the plot. Use the same dictionay keys as penalty_keys or penalty_kernels. If None, it is automatically infered. If False or not in the dictionary, no vertical line at the lower border is drawn.

  • size_factor (float) – Factor for scaling the figure size.

  • legend_size (float) – Matplotlib legend size.

  • show (bool) – Whether to display the plot.

  • save (Optional[str]) – Save the plot to path.

Return type

None

Returns: