msreport 0.0.30__py3-none-any.whl → 0.0.32__py3-none-any.whl

msreport/__init__.py

@@ -8,4 +8,4 @@ from msreport.fasta import import_protein_database
 from msreport.qtable import Qtable
 from msreport.reader import FragPipeReader, MaxQuantReader, SpectronautReader
 
-__version__ = "0.0.30"
+__version__ = "0.0.32"

msreport/aggregate/__init__.py

@@ -0,0 +1,10 @@
+"""A comprehensive set of tools for aggregating and reshaping tabular proteomics data.
+
+The `aggregation` module contains submodules that offer functionalities to transform
+data from lower levels of abstraction (e.g. ions, peptides) to higher levels (e.g.
+peptides, proteins, PTMs) through various summarization and condensation techniques.
+It also includes methods for reshaping tables from "long" to "wide" format, a common
+prerequisite for aggregation. The MaxLFQ algorithm is integrated for specific
+quantitative summarizations, enabling users to build customized, higher-level data
+tables.
+"""

msreport/aggregate/condense.py

@@ -1,3 +1,12 @@
+"""Low-level functions for aggregating numerical and string data.
+
+This module defines fundamental "condenser" functions that operate directly on NumPy
+arrays. These functions are designed to be applied to groups of data, performing
+operations such as summing values, finding maximum/minimum, counting or joining unique
+elements, and calculating abundance profiles. It includes the core implementations for
+MaxLFQ summation.
+"""
+
 import numpy as np
 
 import msreport.helper.maxlfq as MAXLFQ

msreport/aggregate/pivot.py

@@ -1,4 +1,12 @@
-from typing import Iterable, Union
+"""Functionalities for reshaping tabular quantitative proteomics data.
+
+This module offers methods to transform data from a "long" format into a "wide" format,
+which is a common and often necessary step before aggregation or analysis. It supports
+pivoting data based on specified index and grouping columns, and can handle both
+quantitative values and annotation columns.
+"""
+
+from typing import Iterable
 
 import pandas as pd
 
@@ -12,11 +20,12 @@ def pivot_table(
     group_by: str,
     annotation_columns: Iterable[str],
     pivoting_columns: Iterable[str],
-):
+) -> pd.DataFrame:
     """Generates a pivoted table in wide format.
 
     Args:
-        table: Dataframe in long format that is used to generate a table in wide format.
+        long_table: Dataframe in long format that is used to generate a table in wide
+            format.
         index: One or multiple column names that are used to group the table for
             pivoting.
         group_by: Column that is used to split the table on its unique entries.
@@ -58,7 +67,7 @@ def pivot_table(
 
 
 def pivot_column(
-    table: pd.DataFrame, index: Union[str, Iterable], group_by: str, values: str
+    table: pd.DataFrame, index: str | Iterable[str], group_by: str, values: str
 ) -> pd.DataFrame:
     """Returns a reshaped dataframe, generated by pivoting the table on one column.
 
@@ -98,7 +107,7 @@ def pivot_column(
 
 
 def join_unique(
-    table: pd.DataFrame, index: Union[str, Iterable], values: str
+    table: pd.DataFrame, index: str | Iterable[str], values: str
 ) -> pd.DataFrame:
     """Returns a new dataframe with unique values from a column and grouped by 'index'.
 

msreport/aggregate/summarize.py

@@ -1,4 +1,14 @@
-from typing import Callable, Iterable, Optional, Union
+"""High-level functions for aggregating quantitative proteomics data.
+
+This module offers functions to summarize data from a lower level of abstraction (e.g.
+ions, peptides) to a higher level (e.g., peptides, proteins, PTMs). It operates directly
+on pandas DataFrames, allowing users to specify a grouping column and the columns to be
+summarized. These functions often leverage low-level condenser operations defined in
+`msreport.aggregate.condense`. It includes specific functions for MaxLFQ summation, as
+well as general counting, joining, and summing of columns.
+"""
+
+from typing import Callable, Iterable, Optional
 
 import numpy as np
 import pandas as pd
@@ -10,7 +20,7 @@ from msreport.helper import find_sample_columns
 def count_unique(
     table: pd.DataFrame,
     group_by: str,
-    input_column: Union[str, Iterable],
+    input_column: str | Iterable[str],
     output_column: str = "Unique counts",
     is_sorted: bool = False,
 ) -> pd.DataFrame:
@@ -55,7 +65,7 @@ def count_unique(
 def join_unique(
     table: pd.DataFrame,
     group_by: str,
-    input_column: Union[str, Iterable],
+    input_column: str | Iterable[str],
     output_column: str = "Unique values",
     sep: str = ";",
     is_sorted: bool = False,
@@ -215,7 +225,7 @@ def sum_columns_maxlfq(
 def aggregate_unique_groups(
     table: pd.DataFrame,
     group_by: str,
-    columns_to_aggregate: Union[str, Iterable],
+    columns_to_aggregate: str | Iterable[str],
     condenser: Callable,
     is_sorted: bool,
 ) -> tuple[np.ndarray, np.ndarray]:

msreport/analyze.py

@@ -1,12 +1,16 @@
-"""The analyze module contains methods for analysing quantification results."""
+"""Tools for post-processing and statistical analysis of `Qtable` data.
 
-from __future__ import annotations
+All functions in this module take a `Qtable` object and modify its data in place. The
+module provides functionality for data evaluation, normalization, imputation of missing
+values, and statistical testing, including integration with R's LIMMA package.
+"""
 
 import warnings
 from typing import Iterable, Optional, Protocol, Sequence
 
 import numpy as np
 import pandas as pd
+from typing_extensions import Self
 
 import msreport.normalize
 from msreport.errors import OptionalDependencyError
@@ -24,7 +28,7 @@ except OptionalDependencyError as err:
 
 
 class Transformer(Protocol):
-    def fit(self, table: pd.DataFrame) -> Transformer:
+    def fit(self, table: pd.DataFrame) -> Self:
         """Fits the Transformer and returns a fitted Transformer instance."""
 
     def is_fitted(self) -> bool:
@@ -35,7 +39,7 @@ class Transformer(Protocol):
 
 
 class CategoryTransformer(Protocol):
-    def fit(self, table: pd.DataFrame) -> Transformer:
+    def fit(self, table: pd.DataFrame) -> Self:
         """Fits the Transformer and returns a fitted Transformer instance."""
 
     def is_fitted(self) -> bool:
@@ -162,7 +166,7 @@ def validate_proteins(
 
 
 def apply_transformer(
-    qtable: msreport.Qtable,
+    qtable: Qtable,
     transformer: Transformer,
     tag: str,
     exclude_invalid: bool,
@@ -205,6 +209,64 @@ def apply_transformer(
     qtable.data[data_table.columns] = data_table
 
 
+def apply_category_transformer(
+    qtable: Qtable,
+    transformer: CategoryTransformer,
+    tag: str,
+    exclude_invalid: bool,
+    remove_invalid: bool,
+    new_tag: Optional[str] = None,
+) -> None:
+    """Apply a category transformer to Qtable columns selected by tag.
+
+    Args:
+        qtable: A Qtable instance, to which the transformer is applied.
+        transformer: The CategoryTransformer to apply.
+        tag: The tag used to identify the columns for applying the transformer.
+        exclude_invalid: Exclude invalid values from the transformation.
+        remove_invalid: Remove invalid values from the table after the transformation.
+        new_tag: Optional, if specified than the tag is replaced with this value in the
+            column names and the transformed data is stored to these new columns.
+
+    Raises:
+        KeyError: If the category column of the `transformer` is not found in the
+            `qtable.data`.
+        ValueError: If no sample columns are found for the specified tag.
+    """
+    category_column = transformer.get_category_column()
+    if category_column not in qtable.data.columns:
+        raise KeyError(
+            f'The category column "{category_column}" in the transformer '
+            f"is not found in `qtable.data`."
+        )
+
+    valid = qtable.data["Valid"]
+    samples = qtable.get_samples()
+    sample_columns = find_sample_columns(qtable.data, tag, samples)
+
+    if not sample_columns:
+        raise ValueError(f"No sample columns found for tag '{tag}'.")
+
+    if new_tag is not None:
+        sample_columns = [c.replace(tag, new_tag) for c in sample_columns]
+    column_mapping = dict(zip(samples, sample_columns))
+
+    data_table = qtable.make_sample_table(tag, samples_as_columns=True)
+    data_table[category_column] = qtable.data[category_column]
+
+    if exclude_invalid:
+        data_table.loc[valid, :] = transformer.transform(data_table.loc[valid, :])
+    else:
+        data_table = transformer.transform(data_table)
+    data_table = data_table.drop(columns=[category_column])
+
+    if remove_invalid:
+        data_table[~valid] = np.nan
+
+    data_table.columns = [column_mapping[s] for s in data_table.columns]
+    qtable.data[data_table.columns] = data_table
+
+
 def normalize_expression(
     qtable: Qtable,
     normalizer: Transformer,

msreport/export.py

@@ -1,19 +1,13 @@
-"""
-Columns that are not yet present in the amica output at the moment:
-Index([
-    'Protein Probability',
-    'Top Peptide Probability',
-    'Total peptides',
-    'Leading proteins',
-    'Protein entry name',
-    'Fasta header',
-    'Protein length',
-    'iBAQ peptides',
-    'Sequence coverage',
-], dtype='object')
+"""Exporting of proteomics data from `Qtable` into external formats.
+
+This module offers functionalities to convert and save `Qtable` data into files
+compatible with external tools (Amica and Perseus), and creating sequence coverage maps
+in HTML format. While most functions operate on `Qtable` instances, some may accept
+other data structures.
 """
 
 import os
+import pathlib
 import warnings
 from collections import defaultdict as ddict
 from typing import Iterable, Optional, Protocol, Sequence
@@ -99,7 +93,7 @@ def contaminants_to_clipboard(qtable: Qtable) -> None:
 
 def to_perseus_matrix(
     qtable: Qtable,
-    directory,
+    directory: str | pathlib.Path,
     table_name: str = "perseus_matrix.tsv",
 ) -> None:
     """Exports a qtable to a perseus matrix file in tsv format.
@@ -151,7 +145,7 @@ def to_perseus_matrix(
 
 def to_amica(
     qtable: Qtable,
-    directory,
+    directory: str | pathlib.Path,
     table_name: str = "amica_table.tsv",
     design_name: str = "amica_design.tsv",
 ) -> None:
@@ -508,7 +502,7 @@ def _find_covered_region_boundaries(
     Examples:
         >>> coverage_mask = [True, True, False, False, True]
         >>> _find_covered_region_boundaries(coverage_mask)
-        ... [(0, 1), (4, 4)]
+        [(0, 1), (4, 4)]
     """
     start = []
     stop = []

msreport/fasta.py

@@ -1,11 +1,18 @@
+"""Functionalities for import and access to protein sequence databases from FASTA files.
+
+This module serves as an interface to the `profasta` library, offering a convenient way
+to generate a `profasta.db.ProteinDatabase` from one or multiple FASTA files. It
+supports custom FASTA header parsing through a configurable header parser.
+"""
+
 import pathlib
-from typing import Iterable, Union
+from typing import Iterable
 
 from profasta.db import ProteinDatabase
 
 
 def import_protein_database(
-    fasta_path: Union[str, pathlib.Path, Iterable[Union[str, pathlib.Path]]],
+    fasta_path: str | pathlib.Path | Iterable[str | pathlib.Path],
     header_parser: str = "uniprot",
 ) -> ProteinDatabase:
     """Generates a protein database from one or a list of fasta files.

msreport/helper/__init__.py

@@ -1,3 +1,9 @@
+"""A collection of widely used helper and utility functions.
+
+This module re-exports commonly used functions from various `msreport.helper`
+submodules for convenience.
+"""
+
 from .calc import (
     calculate_monoisotopic_mass,
     calculate_sequence_coverage,
@@ -21,3 +27,15 @@ from .temp import (
     extract_modifications,
     modify_peptide,
 )
+
+__all__ = [
+    "apply_intensity_cutoff",
+    "find_columns",
+    "find_sample_columns",
+    "guess_design",
+    "intensities_in_logspace",
+    "keep_rows_by_partial_match",
+    "remove_rows_by_partial_match",
+    "rename_mq_reporter_channels",
+    "rename_sample_columns",
+]

msreport/helper/maxlfq.py

@@ -113,9 +113,9 @@ def calculate_pairwise_mode_log_ratio_matrix(
         ...     ]
         ... )
         >>> calculate_pairwise_mode_log_ratio_matrix(array)
-        array([[ 0.       , -0.0849625, -1.       ],
-               [ 0.0849625,  0.       , -1.       ],
-               [ 1.       ,  1.       ,  0.       ]])
+        array([[ 0.        , -0.08496251, -1.       ],
+               [ 0.08496251,  0.       , -1.       ],
+               [ 1.        ,  1.       ,  0.       ]])
     """
     ratio_marix = _calculate_pairwise_centered_log_ratio_matrix(
         array, msreport.helper.mode, log_transformed=log_transformed

msreport/impute.py

@@ -1,9 +1,17 @@
-from __future__ import annotations
+"""Transformer classes for imputing missing values in quantitative proteomics data.
+
+This module defines transformer classes that can be fitted to a table containing
+quantitative values to learn imputation parameters. Once fitted, these transformers can
+then be applied to another table to transform it by filling in missing values. The
+transformation returns a new copy of the table with the imputed values, leaving the
+original table unchanged.
+"""
 
 from typing import Any, Optional
 
 import numpy as np
 import pandas as pd
+from typing_extensions import Self
 
 from msreport.errors import NotFittedError
 
@@ -42,7 +50,7 @@ class FixedValueImputer:
         self.column_wise = column_wise
         self._sample_fill_values: dict[str, float] = {}
 
-    def fit(self, table: pd.DataFrame) -> FixedValueImputer:
+    def fit(self, table: pd.DataFrame) -> Self:
         """Fits the FixedValueImputer.
 
         Args:
@@ -79,7 +87,7 @@ class FixedValueImputer:
         Returns:
             'table' with imputed missing values.
         """
-        confirm_is_fitted(self)
+        _confirm_is_fitted(self)
 
         _table = table.copy()
         for column in _table.columns:
@@ -108,7 +116,7 @@ class GaussianImputer:
         self.sigma = sigma
         self.seed = seed
 
-    def fit(self, table: pd.DataFrame) -> GaussianImputer:
+    def fit(self, table: pd.DataFrame) -> Self:
         """Fits the GaussianImputer, altough this is not necessary.
 
         Args:
@@ -134,7 +142,7 @@ class GaussianImputer:
         Returns:
             'table' with imputed missing values.
         """
-        confirm_is_fitted(self)
+        _confirm_is_fitted(self)
         np.random.seed(self.seed)
 
         _table = table.copy()
@@ -182,9 +190,9 @@ class PerseusImputer:
         self.std_width = std_width
         self.column_wise = column_wise
         self.seed = seed
-        self._column_params: dict[str, dict] = {}
+        self._column_params: dict[str, dict[str, float]] = {}
 
-    def fit(self, table: pd.DataFrame) -> PerseusImputer:
+    def fit(self, table: pd.DataFrame) -> Self:
         """Fits the PerseusImputer.
 
         Args:
@@ -223,7 +231,7 @@ class PerseusImputer:
         Returns:
             'table' with imputed missing values.
         """
-        confirm_is_fitted(self)
+        _confirm_is_fitted(self)
         np.random.seed(self.seed)
 
         _table = table.copy()
@@ -239,7 +247,7 @@ class PerseusImputer:
         return _table
 
 
-def confirm_is_fitted(imputer: Any, msg: Optional[str] = None) -> None:
+def _confirm_is_fitted(imputer: Any, msg: Optional[str] = None) -> None:
     """Perform is_fitted validation for imputer instances.
 
     Checks if the imputer is fitted by verifying the presence of fitted attributes
@@ -266,7 +274,7 @@ def confirm_is_fitted(imputer: Any, msg: Optional[str] = None) -> None:
         raise NotFittedError(msg % {"name": type(imputer).__name__})
 
 
-def _calculate_integer_below_min(table) -> int:
+def _calculate_integer_below_min(table: pd.DataFrame) -> int:
     minimal_value = np.nanmin(table.to_numpy().flatten())
     below_minimal = np.floor(minimal_value)
     if minimal_value <= below_minimal:

msreport/isobar.py

@@ -1,34 +1,31 @@
-from __future__ import annotations
+"""Provides a transformer class for processing isobarically labeled proteomics data.
+
+This module defines the `IsotopeImpurityCorrecter` class for processing of isobaric
+(e.g., TMT, iTRAQ) reporter intensities. This transformer must be fitted with an isotope
+impurity matrix to correct interference in reporter intensities. Once fitted, the
+transformer can then be applied to a table containing reporter ion intensities to adjust
+its intensity values. The transformation returns a new copy of the table with the
+processed values, leaving the original table unchanged.
+"""
 
 import functools
-from typing import Protocol
 
 import numpy as np
 import pandas as pd
 import scipy
+from typing_extensions import Self
 
 import msreport.helper
 from msreport.errors import NotFittedError
 
 
-class Transformer(Protocol):
-    def fit(self, table: pd.DataFrame) -> Transformer:
-        """Fits the Transformer and returns a fitted Transformer instance."""
-
-    def is_fitted(self) -> bool:
-        """Returns True if the Transformer has been fitted."""
-
-    def transform(self, table: pd.DataFrame) -> pd.DataFrame:
-        """Transform values in 'table'."""
-
-
 class IsotopeImpurityCorrecter:
     """Corrects isotope impurity interference in isobaric reporter expression values."""
 
     def __init__(self):
         self._impurity_matrix = None
 
-    def fit(self, impurity_matrix: np.ndarray) -> IsotopeImpurityCorrecter:
+    def fit(self, impurity_matrix: np.ndarray) -> Self:
         """Fits the isotope impurity correcter to a given impurity matrix.
 
         Args:

msreport/normalize.py

@@ -1,4 +1,16 @@
-from __future__ import annotations
+"""Transformer classes for normalizing and transforming quantitative proteomics data.
+
+This module defines various transformer classes for normalizing and scaling quantitative
+values in tabular data. Examples include normalizers like median, mode, and LOWESS, as
+well as scalers such as PercentageScaler and ZScoreScaler. A specialized
+`CategoricalNormalizer` is also provided, which, when appropriately fitted and applied,
+can be used for complex transformations such as iBAQ or site-to-protein normalization.
+
+These transformers can be fitted to a table containing quantitative values to learn
+parameters. Once fitted, they can then be applied to another table to adjust its values.
+The transformation returns a new copy of the table with the normalized/scaled values,
+leaving the original table unchanged.
+"""
 
 from typing import Callable, Iterable, Optional, Protocol
 
@@ -79,7 +91,7 @@ class FixedValueNormalizer:
         Raises:
             NotFittedError: If the FixedValueNormalizer has not been fitted yet.
         """
-        confirm_is_fitted(self)
+        _confirm_is_fitted(self)
         return self._sample_fits.copy()
 
     def transform(self, table: pd.DataFrame) -> pd.DataFrame:
@@ -95,7 +107,7 @@ class FixedValueNormalizer:
         Raises:
             NotFittedError: If the FixedValueNormalizer has not been fitted yet.
         """
-        confirm_is_fitted(self)
+        _confirm_is_fitted(self)
 
         _table = table.copy()
         for column in _table.columns:
@@ -195,7 +207,7 @@ class ValueDependentNormalizer:
         Raises:
             NotFittedError: If the ValueDependentNormalizer has not been fitted yet.
         """
-        confirm_is_fitted(self)
+        _confirm_is_fitted(self)
         return self._sample_fits.copy()
 
     def transform(self, table: pd.DataFrame) -> pd.DataFrame:
@@ -211,7 +223,7 @@ class ValueDependentNormalizer:
         Raises:
             NotFittedError: If the ValueDependentNormalizer has not been fitted yet.
         """
-        confirm_is_fitted(self)
+        _confirm_is_fitted(self)
 
         _table = table.copy()
         for column in _table.columns:
@@ -250,6 +262,59 @@ class ValueDependentNormalizer:
             self._sample_fits[sample] = sample_fit
 
 
+class SumNormalizer:
+    """Normalizer that uses the sum of all values in each sample for normalization.
+
+    Expects log2-transformed intensity values. To obtain normalization factors, the sum
+    of non-log2-transformed values is calculated for each sample, then divided by the
+    average of all sample sums and log2-transformed.
+    """
+
+    def __init__(self):
+        """Initializes the SumNormalizer."""
+        self._sample_fits: dict[str, float] = {}
+
+    def fit(self, table: pd.DataFrame) -> Self:
+        """Fits the SumNormalizer and returns a fitted instance.
+
+        Args:
+            table: Dataframe used to calculate normalization values for each column.
+
+        Returns:
+            Returns the instance itself.
+        """
+        _sums = np.power(2, table).sum()
+        _log2_fits = np.log2(_sums.divide(_sums.mean()))
+        self._sample_fits = _log2_fits.to_dict()
+        return self
+
+    def is_fitted(self) -> bool:
+        """Returns True if the Transformer has been fitted."""
+        return True if self._sample_fits else False
+
+    def get_fits(self) -> dict[str, float]:
+        """Returns a dictionary containing the fitted center values per sample.
+
+        Raises:
+            NotFittedError: If the FixedValueNormalizer has not been fitted yet.
+        """
+        _confirm_is_fitted(self)
+        return self._sample_fits.copy()
+
+    def transform(self, table: pd.DataFrame) -> pd.DataFrame:
+        """Transform values in table."""
+        _confirm_is_fitted(self)
+
+        _table = table.copy()
+        for column in _table.columns:
+            column_data = np.array(_table[column], dtype=float)
+            mask = np.isfinite(column_data)
+            column_data[mask] = column_data[mask] - self._sample_fits[column]
+
+            _table[column] = column_data
+        return _table
+
+
 class MedianNormalizer(FixedValueNormalizer):
     """A FixedValueNormalizer that uses the median as the fitting function.
 
@@ -346,7 +411,7 @@ class CategoricalNormalizer:
         Raises:
             NotFittedError: If the CategoricalNormalizer has not been fitted yet.
         """
-        confirm_is_fitted(self)
+        _confirm_is_fitted(self)
         return self._fitted_table.copy()
 
     def get_category_column(self) -> str:
@@ -367,7 +432,7 @@ class CategoricalNormalizer:
                 table.
             NotFittedError: If the CategoricalNormalizer has not been fitted yet.
         """
-        confirm_is_fitted(self)
+        _confirm_is_fitted(self)
 
         original_index = table.index
         table = table.set_index(self.get_category_column(), drop=True, inplace=False)
@@ -396,11 +461,11 @@ class PercentageScaler:
         return self
 
     def is_fitted(self) -> bool:
-        """Always returns True because the ZscoreScaler does not need to be fitted."""
+        """Always returns True because the Scaler does not need to be fitted."""
         return True
 
     def get_fits(self) -> dict:
-        """Returns a dictionary containing the parameters 'with_mean' and 'with_std'."""
+        """Returns an empty dictionary."""
         return {}
 
     def transform(self, table: pd.DataFrame) -> pd.DataFrame:
@@ -457,7 +522,27 @@ class ZscoreScaler:
         return scaled_table
 
 
-def confirm_is_fitted(
+class Log2Transformer:
+    """Apply log2 transformation to column values."""
+
+    def fit(self, table: pd.DataFrame) -> Self:
+        """Returns the instance itself."""
+        return self
+
+    def is_fitted(self) -> bool:
+        """Returns True if the transformer is fitted."""
+        return True
+
+    def transform(self, table: pd.DataFrame) -> pd.DataFrame:
+        """Applies a log2 transformation to each column of the table.
+
+        Zero values are replaced with NaN before the transformation to avoid an error
+        during the log2 calculation.
+        """
+        return pd.DataFrame(np.log2(table.replace({0: np.nan})))
+
+
+def _confirm_is_fitted(
     normalizer: AbstractTransformer, msg: Optional[str] = None
 ) -> None:
     """Perform is_fitted validation for normalizer instances.