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Base

Includes foundational methods for the base pAnnData object.

BaseMixin

Core base methods for pAnnData.

This mixin provides essential utility and management functions for cloning, checking, and managing core attributes of a pAnnData object. These methods serve as foundational building blocks for other mixins and functions.

Features:

  • Checks presence of data (.prot or .pep)
  • Safe object copying with state preservation
  • Internal metadata management (stats, history, summary)

Methods:

Name Description
_has_data

Check whether .prot and/or .pep data are present

copy

Return a new pAnnData object with retained internal state
Source code in src/scpviz/pAnnData/base.py 
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class BaseMixin:
    """
    Core base methods for pAnnData.

    This mixin provides essential utility and management functions for cloning, 
    checking, and managing core attributes of a `pAnnData` object. These methods
    serve as foundational building blocks for other mixins and functions.

    Features:

    - Checks presence of data (.prot or .pep)
    - Safe object copying with state preservation
    - Internal metadata management (stats, history, summary)

    Functions:
        _has_data: Check whether .prot and/or .pep data are present  
        copy: Return a new `pAnnData` object with retained internal state
    """
    def _has_data(self) -> bool:
        """
        Check whether the pAnnData object contains either protein or peptide data.

        Returns:
            bool: True if either .prot or .pep is not None; otherwise False.
        """
        return self.prot is not None or self.pep is not None # type: ignore[attr-defined]

    def copy(self):
        """
        Return a new `pAnnData` object with the current state of all components.

        This method performs a shallow copy of core data (.prot, .pep) and a deep copy of internal attributes
        (e.g., RS matrix, summary, stats, and cached maps). It avoids full deepcopy for efficiency and retains
        the current filtered or processed state of the object.

        Returns:
            pAnnData: A new object containing copies of the current data and metadata.
        """
        new_obj = self.__class__.__new__(self.__class__)

        # Copy core AnnData components
        new_obj.prot = self.prot.copy() if self.prot is not None else None # type: ignore[attr-defined]
        new_obj.pep = self.pep.copy() if self.pep is not None else None # type: ignore[attr-defined]
        new_obj._rs = copy.deepcopy(self._rs) # type: ignore[attr-defined]

        # Copy summary and stats
        new_obj._stats = copy.deepcopy(self._stats) # type: ignore[attr-defined]
        new_obj._history = copy.deepcopy(self._history) # type: ignore[attr-defined]
        new_obj._previous_summary = copy.deepcopy(self._previous_summary) # type: ignore[attr-defined]
        new_obj._suppress_summary_log = True # type: ignore[attr-defined]
        new_obj.summary = self._summary.copy(deep=True) if self._summary is not None else None # go through setter to mark as stale, # type: ignore[attr-defined]
        del new_obj._suppress_summary_log # type: ignore[attr-defined]

        # Optional: cached maps
        if hasattr(self, "_gene_maps_protein"):
            new_obj._gene_maps_protein = copy.deepcopy(self._gene_maps_protein) # type: ignore[attr-defined]
        if hasattr(self, "_protein_maps_peptide"):
            new_obj._protein_maps_peptide = copy.deepcopy(self._protein_maps_peptide) # type: ignore[attr-defined]

        return new_obj

    def compare_current_to_raw(self, on="protein"):
        """
        Compare current pdata object to original raw data, showing how many samples and features were dropped.
        Compares current obs/var names to the original raw data (stored in .uns).

        Args:
            on (str): Dataset to compare ('protein' or 'peptide').

        Returns:
            dict: Dictionary summarizing dropped samples and features.
        """
        print(f"{format_log_prefix('user', 1)} Comparing current pdata to X_raw [{on}]:")

        adata = getattr(self, "prot" if on == "protein" else "pep", None)
        if adata is None:
            print(f"{format_log_prefix('warn', 2)} No {on} data found.")
            return None

        orig_obs = set(adata.uns.get("X_raw_obs_names", []))
        orig_var = set(adata.uns.get("X_raw_var_names", []))
        current_obs = set(adata.obs_names)
        current_var = set(adata.var_names)

        dropped_obs = sorted(list(orig_obs - current_obs))
        dropped_var = sorted(list(orig_var - current_var))

        print(f"   → Samples dropped: {len(dropped_obs)}")
        print(f"   → Features dropped: {len(dropped_var)}")

        return {"dropped_samples": dropped_obs, "dropped_features": dropped_var}

compare_current_to_raw 

compare_current_to_raw(on='protein')

Compare current pdata object to original raw data, showing how many samples and features were dropped. Compares current obs/var names to the original raw data (stored in .uns).

Parameters:

Name Type Description Default
on str

Dataset to compare ('protein' or 'peptide').

 'protein'

Returns:

Name Type Description
dict

Dictionary summarizing dropped samples and features.
Source code in src/scpviz/pAnnData/base.py 
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def compare_current_to_raw(self, on="protein"):
    """
    Compare current pdata object to original raw data, showing how many samples and features were dropped.
    Compares current obs/var names to the original raw data (stored in .uns).

    Args:
        on (str): Dataset to compare ('protein' or 'peptide').

    Returns:
        dict: Dictionary summarizing dropped samples and features.
    """
    print(f"{format_log_prefix('user', 1)} Comparing current pdata to X_raw [{on}]:")

    adata = getattr(self, "prot" if on == "protein" else "pep", None)
    if adata is None:
        print(f"{format_log_prefix('warn', 2)} No {on} data found.")
        return None

    orig_obs = set(adata.uns.get("X_raw_obs_names", []))
    orig_var = set(adata.uns.get("X_raw_var_names", []))
    current_obs = set(adata.obs_names)
    current_var = set(adata.var_names)

    dropped_obs = sorted(list(orig_obs - current_obs))
    dropped_var = sorted(list(orig_var - current_var))

    print(f"   → Samples dropped: {len(dropped_obs)}")
    print(f"   → Features dropped: {len(dropped_var)}")

    return {"dropped_samples": dropped_obs, "dropped_features": dropped_var}

copy 

copy()

Return a new pAnnData object with the current state of all components.

This method performs a shallow copy of core data (.prot, .pep) and a deep copy of internal attributes (e.g., RS matrix, summary, stats, and cached maps). It avoids full deepcopy for efficiency and retains the current filtered or processed state of the object.

Returns:

Name Type Description
pAnnData

A new object containing copies of the current data and metadata.
Source code in src/scpviz/pAnnData/base.py 
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def copy(self):
    """
    Return a new `pAnnData` object with the current state of all components.

    This method performs a shallow copy of core data (.prot, .pep) and a deep copy of internal attributes
    (e.g., RS matrix, summary, stats, and cached maps). It avoids full deepcopy for efficiency and retains
    the current filtered or processed state of the object.

    Returns:
        pAnnData: A new object containing copies of the current data and metadata.
    """
    new_obj = self.__class__.__new__(self.__class__)

    # Copy core AnnData components
    new_obj.prot = self.prot.copy() if self.prot is not None else None # type: ignore[attr-defined]
    new_obj.pep = self.pep.copy() if self.pep is not None else None # type: ignore[attr-defined]
    new_obj._rs = copy.deepcopy(self._rs) # type: ignore[attr-defined]

    # Copy summary and stats
    new_obj._stats = copy.deepcopy(self._stats) # type: ignore[attr-defined]
    new_obj._history = copy.deepcopy(self._history) # type: ignore[attr-defined]
    new_obj._previous_summary = copy.deepcopy(self._previous_summary) # type: ignore[attr-defined]
    new_obj._suppress_summary_log = True # type: ignore[attr-defined]
    new_obj.summary = self._summary.copy(deep=True) if self._summary is not None else None # go through setter to mark as stale, # type: ignore[attr-defined]
    del new_obj._suppress_summary_log # type: ignore[attr-defined]

    # Optional: cached maps
    if hasattr(self, "_gene_maps_protein"):
        new_obj._gene_maps_protein = copy.deepcopy(self._gene_maps_protein) # type: ignore[attr-defined]
    if hasattr(self, "_protein_maps_peptide"):
        new_obj._protein_maps_peptide = copy.deepcopy(self._protein_maps_peptide) # type: ignore[attr-defined]

    return new_obj