mosaicmpi.integration.Integration.get_category_overrepresentation

mosaicmpi.integration.Integration.get_category_overrepresentation#

Integration.get_category_overrepresentation(layer: str, subset_datasets: str | Iterable[str] | None = None, truncate_negative: bool = True, subset_categories: Collection[str] = None) → DataFrame#

Calculate Pearson residual of chi-squared test, associating programs for each rank (k) to categories of samples/observations. By default, truncates negative values.

Parameters:

  • layer (str) – name of categorical data layer

  • subset_datasets (str or Iterable[str], optional) – dataset name or iterable of dataset names to subset the results, defaults to None

  • truncate_negative (bool, optional) – Truncate negative residuals to 0, defaults to True

  • subset_categories (Collection[str]) – Provide a subset of categories for calculating overrepresentation

Returns:

category × programs matrix of overrepresentation values

Return type:

pd.DataFrame

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