msreport 0.0.26__py3-none-any.whl → 0.0.27__py3-none-any.whl

msreport/__init__.py

@@ -10,4 +10,4 @@ import msreport.normalize
 import msreport.plot
 import msreport.reader
 
-__version__ = "0.0.26"
+__version__ = "0.0.27"

msreport/analyze.py

@@ -9,7 +9,7 @@ import pandas as pd
 
 import msreport.normalize
 import msreport.rinterface
-from msreport.qtable import Qtable
+from msreport.helper import find_sample_columns
 
 
 class Transformer(Protocol):
@@ -33,8 +33,8 @@ class CategoryTransformer(Protocol):
     def transform(self, table: pd.DataFrame) -> pd.DataFrame:
         """Transform values in 'table'."""
 
-    def get_category_column(self, table: pd.DataFrame) -> pd.DataFrame:
-        """Returns the specified category column."""
+    def get_category_column(self) -> str:
+        """Returns the name of the category column."""
 
 
 def analyze_missingness(qtable: Qtable) -> None:
@@ -75,6 +75,7 @@ def analyze_missingness(qtable: Qtable) -> None:
 def validate_proteins(
     qtable: Qtable,
     min_peptides: int = 0,
+    min_spectral_counts: int = 0,
     remove_contaminants: bool = True,
     min_events: Optional[int] = None,
     max_missing: Optional[int] = None,
@@ -84,12 +85,13 @@ def validate_proteins(
     Adds an additional column "Valid" to the qtable, containing Boolean values.
 
     Requires expression columns to be set. Depending on the arguments requires the
-    columns "Total peptides", "Potential contaminant", and the experiment columns
-    "Missing experiment_name" and "Events experiment_name".
+    columns "Total peptides", "Spectral count Combined", "Potential contaminant", and
+    the experiment columns "Missing experiment_name" and "Events experiment_name".
 
     Args:
         qtable: A Qtable instance.
         min_peptides: Minimum number of unique peptides, default 0.
+        min_spectral_counts: Minimum number of combined spectral counts, default 0.
         remove_contaminants: If true, the "Potential contaminant" column is used to
             remove invalid entries, default True. If no "Potential contaminant" column
             is present 'remove_contaminants' is ignored.
@@ -107,6 +109,16 @@ def validate_proteins(
             [valid_entries, qtable["Total peptides"] >= min_peptides], axis=0
         )
 
+    if min_spectral_counts > 0:
+        if "Spectral count Combined" not in qtable:
+            raise KeyError(
+                "'Spectral count Combined' column not present in qtable.data"
+            )
+        valid_entries = np.all(
+            [valid_entries, qtable["Spectral count Combined"] >= min_spectral_counts],
+            axis=0,
+        )
+
     # TODO: not tested from here #
     if remove_contaminants:
         if "Potential contaminant" not in qtable:
@@ -138,6 +150,50 @@ def validate_proteins(
     qtable["Valid"] = valid_entries
 
 
+def apply_transformer(
+    qtable: msreport.Qtable,
+    transformer: Transformer,
+    tag: str,
+    exclude_invalid: bool,
+    remove_invalid: bool,
+    new_tag: Optional[str] = None,
+) -> None:
+    """Applies a transformer to the values of a Qtable selected with the tag parameter.
+
+    Args:
+        qtable: A Qtable instance, to which the transformer is applied.
+        transformer: The transformer 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.
+    """
+    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)
+
+    if exclude_invalid:
+        data_table[valid] = transformer.transform(data_table[valid])
+    else:
+        data_table = transformer.transform(data_table)
+
+    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,
@@ -168,11 +224,9 @@ def normalize_expression(
     raw_data = table[sample_columns]
     if not normalizer.is_fitted():
         if exclude_invalid:
-            valid_mask = table["Valid"]
+            normalizer.fit(raw_data[table["Valid"]])
         else:
-            valid_mask = np.ones_like(table["Valid"], dtype=bool)
-        fit_data = raw_data[valid_mask]
-        normalizer = normalizer.fit(fit_data)
+            normalizer = normalizer.fit(raw_data)
 
     transformed_data = normalizer.transform(raw_data)
     qtable[expression_columns] = transformed_data[sample_columns]
@@ -421,7 +475,7 @@ def two_group_comparison(
 
 def calculate_multi_group_limma(
     qtable: Qtable,
-    experiment_pairs: list[list[str, str]],
+    experiment_pairs: Iterable[Iterable[str]],
     exclude_invalid: bool = True,
     batch: bool = False,
     limma_trend: bool = True,
@@ -454,6 +508,14 @@ def calculate_multi_group_limma(
         limma_trend: If true, an intensity-dependent trend is fitted to the prior
             variance during calculation of the moderated t-statistics, refer to
             limma.eBayes for details; default True.
+
+    Raises:
+        KeyError: If the "Batch" column is not present in the qtable.design when
+            'batch' is set to True.
+        ValueError: If all values from qtable.design["Batch"] are identical when 'batch'
+            is set to True.
+        ValueError: If the same experiment pair has been specified multiple times in
+            'experiment_pairs'.
     """
     # TODO: not tested #
     if batch and "Batch" not in qtable.get_design():
@@ -466,6 +528,11 @@ def calculate_multi_group_limma(
             "When using calculate_multi_group_limma(batch=True), not all values from"
             ' qtable.design["Batch"] are allowed to be identical.'
         )
+    if len(list(experiment_pairs)) != len(set(experiment_pairs)):
+        raise ValueError(
+            "The same experiment pair has been specified multiple times."
+            " Each entry in the `experiment_pairs` argument must be unique."
+        )
 
     design = qtable.get_design()
     table = qtable.make_expression_table(
@@ -504,7 +571,7 @@ def calculate_multi_group_limma(
         limma_result.rename(columns=mapping, inplace=True)
 
     limma_table = pd.DataFrame(index=table.index)
-    limma_table = limma_table.join(limma_results.values())
+    limma_table = limma_table.join(list(limma_results.values()))
     limma_table.fillna(np.nan, inplace=True)
     qtable.add_expression_features(limma_table)
 
@@ -516,7 +583,7 @@ def calculate_multi_group_limma(
 
 def calculate_two_group_limma(
     qtable: Qtable,
-    experiment_pair: list[str, str],
+    experiment_pair: list[str],
     exclude_invalid: bool = True,
     limma_trend: bool = True,
 ) -> None:
@@ -582,5 +649,3 @@ def calculate_two_group_limma(
     mapping = {col: f"{col} {comparison_group}" for col in limma_table.columns}
     limma_table.rename(columns=mapping, inplace=True)
     qtable.add_expression_features(limma_table)
-
-    return limma_result

msreport/helper/calc.py

@@ -19,22 +19,28 @@ def mode(values: Iterable) -> float:
     Returns:
         The estimated mode. If no finite values are present, returns nan.
     """
-    values = np.array(values)
+    values = np.asarray(values)
     finite_values = values[np.isfinite(values)]
     if len(finite_values) == 0:
-        mode = np.nan
+        return np.nan
     elif len(np.unique(finite_values)) == 1:
-        mode = np.unique(finite_values)[0]
-    else:
-        median = np.median(finite_values)
-        bounds = (median - 1.5, median + 1.5)
-        kde = scipy.stats.gaussian_kde(finite_values)
-        optimize_result = scipy.optimize.minimize_scalar(
-            lambda x: -kde(x)[0], method="Bounded", bounds=bounds
-        )
-        mode = optimize_result.x
-        # Maybe add fallback function if optimize was not successful
-    return mode
+        return np.unique(finite_values)[0]
+
+    kde = scipy.stats.gaussian_kde(finite_values)
+    minimum_function = lambda x: -kde(x)[0]
+
+    min_slice, max_sclice = np.percentile(finite_values, (2, 98))
+    slice_step = 0.2
+    brute_optimize_result = scipy.optimize.brute(
+        minimum_function, [slice(min_slice, max_sclice + slice_step, slice_step)]
+    )
+    rough_minimum = brute_optimize_result[0]
+
+    local_optimize_result = scipy.optimize.minimize(
+        minimum_function, x0=rough_minimum, method="BFGS"
+    )
+    fine_minimum = local_optimize_result.x[0]
+    return fine_minimum
 
 
 def calculate_tryptic_ibaq_peptides(protein_sequence: str) -> int:

msreport/impute.py

@@ -1,5 +1,5 @@
 from __future__ import annotations
-from typing import Optional
+from typing import Optional, Any
 
 import numpy as np
 import pandas as pd
@@ -18,7 +18,7 @@ class FixedValueImputer:
     def __init__(
         self,
         strategy: str,
-        fill_value: Optional[float] = None,
+        fill_value: float = 0.0,
         column_wise: bool = True,
     ):
         """Initializes the FixedValueImputer.
@@ -51,13 +51,11 @@ class FixedValueImputer:
             Returns the fitted FixedValueImputer instance.
         """
         if self.strategy == "constant":
-            # if not isinstance(self.fill_value, (float, int)):
-            #     raise Excpetion()
             fill_values = {column: self.fill_value for column in table.columns}
         elif self.strategy == "below":
             if self.column_wise:
                 fill_values = {}
-                for column in table:
+                for column in table.columns:
                     fill_values[column] = _calculate_integer_below_min(table[column])
             else:
                 int_below_min = _calculate_integer_below_min(table)
@@ -240,7 +238,7 @@ 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

msreport/normalize.py

@@ -1,7 +1,6 @@
 from __future__ import annotations
-import abc
-import itertools
-from typing import Callable, Iterable, Optional
+from typing import Callable, Iterable, Optional, Protocol
+from typing_extensions import Self
 
 import numpy as np
 import pandas as pd
@@ -12,27 +11,18 @@ import msreport.helper.maxlfq as MAXLFQ
 from msreport.errors import NotFittedError
 
 
-class BaseSampleNormalizer(abc.ABC):
-    """Base class for all sample normalizers."""
+class AbstractTransformer(Protocol):
+    def fit(self, table: pd.DataFrame) -> Self:
+        """Fits the Transformer and returns a fitted Transformer instance."""
 
-    @abc.abstractmethod
-    def fit(self, table: pd.DataFrame) -> BaseSampleNormalizer:
-        ...
-
-    @abc.abstractmethod
     def is_fitted(self) -> bool:
-        ...
-
-    @abc.abstractmethod
-    def get_fits(self) -> dict[...]:
-        ...
+        """Returns True if the Transformer has been fitted."""
 
-    @abc.abstractmethod
     def transform(self, table: pd.DataFrame) -> pd.DataFrame:
-        ...
+        """Transform values in table."""
 
 
-class FixedValueNormalizer(BaseSampleNormalizer):
+class FixedValueNormalizer:
     """Normalization by a constant normalization factor for each sample.
 
     Expects log transformed intensity values.
@@ -58,11 +48,11 @@ class FixedValueNormalizer(BaseSampleNormalizer):
                 f'"comparison" = {comparison} not allowed. '
                 'Must be either "paired" or "reference".'
             )
-        self._comparison_mode = comparison
-        self._fit_function = center_function
-        self._sample_fits = None
+        self._comparison_mode: str = comparison
+        self._fit_function: Callable = center_function
+        self._sample_fits: dict[str, float] = {}
 
-    def fit(self, table: pd.DataFrame) -> BaseSampleNormalizer:
+    def fit(self, table: pd.DataFrame) -> Self:
         """Fits the FixedValueNormalizer.
 
         Args:
@@ -80,7 +70,7 @@ class FixedValueNormalizer(BaseSampleNormalizer):
 
     def is_fitted(self) -> bool:
         """Returns True if the FixedValueNormalizer has been fitted."""
-        return self._sample_fits is not None
+        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.
@@ -159,13 +149,13 @@ class FixedValueNormalizer(BaseSampleNormalizer):
             self._sample_fits[sample] = sample_fit
 
 
-class ValueDependentNormalizer(BaseSampleNormalizer):
+class ValueDependentNormalizer:
     """Normalization with a value dependent fit for each sample.
 
     Expects log transformed intensity values.
     """
 
-    def __init__(self, fit_function: Callable):
+    def __init__(self, fit_function: Callable[[Iterable, Iterable], np.ndarray]):
         """Initializes the ValueDependentNormalizer.
 
         Args:
@@ -175,10 +165,10 @@ class ValueDependentNormalizer(BaseSampleNormalizer):
                 with two columns. The first column contains the values and the second
                 column the fitted deviations.
         """
-        self._sample_fits = None
+        self._sample_fits: dict[str, np.ndarray] = {}
         self._fit_function = fit_function
 
-    def fit(self, table: pd.DataFrame) -> BaseSampleNormalizer:
+    def fit(self, table: pd.DataFrame) -> Self:
         """Fits the ValueDependentNormalizer.
 
         Args:
@@ -192,9 +182,9 @@ class ValueDependentNormalizer(BaseSampleNormalizer):
 
     def is_fitted(self) -> bool:
         """Returns True if the ValueDependentNormalizer has been fitted."""
-        return self._sample_fits is not None
+        return True if self._sample_fits else False
 
-    def get_fits(self) -> dict[str, Iterable[float, float]]:
+    def get_fits(self) -> dict[str, np.ndarray]:
         """Returns a dictionary containing lists of fitting data per sample.
 
         Returns:
@@ -324,14 +314,14 @@ class CategoricalNormalizer:
                 column must be present in the reference table and the table to be
                 transformed.
         """
-        self._fitted_table = None
-        self._category_column = category_column
+        self._fitted_table: pd.DataFrame = pd.DataFrame()
+        self._category_column: str = category_column
 
     def is_fitted(self) -> bool:
         """Returns True if the CategoricalNormalizer has been fitted."""
-        return self._fitted_table is not None
+        return not self._fitted_table.empty
 
-    def fit(self, reference_table: pd.DataFrame) -> BaseSampleNormalizer:
+    def fit(self, reference_table: pd.DataFrame) -> Self:
         """Fits the CategoricalNormalizer to a reference table.
 
         Args:
@@ -397,7 +387,34 @@ class CategoricalNormalizer:
         return transformed_table
 
 
-class ZscoreScaler(BaseSampleNormalizer):
+class PercentageScaler:
+    """Transform column values to percentages by dividing them with the column sum."""
+
+    def fit(self, table: pd.DataFrame) -> Self:
+        """Returns the instance itself."""
+        return self
+
+    def is_fitted(self) -> bool:
+        """Always returns True because the ZscoreScaler does not need to be fitted."""
+        return True
+
+    def get_fits(self) -> dict:
+        """Returns a dictionary containing the parameters 'with_mean' and 'with_std'."""
+        return {}
+
+    def transform(self, table: pd.DataFrame) -> pd.DataFrame:
+        """Transforms column values into percentages by devision with the column sum.
+
+        Args:
+            table: The table used to scale row values.
+
+        Returns:
+            A copy of the table containing the scaled values.
+        """
+        return table.divide(table.sum(axis=0), axis=1)
+
+
+class ZscoreScaler:
     """Normalize samples by z-score scaling."""
 
     def __init__(self, with_mean: bool = True, with_std: bool = True):
@@ -410,7 +427,7 @@ class ZscoreScaler(BaseSampleNormalizer):
         self._with_mean = with_mean
         self._with_std = with_std
 
-    def fit(self, table: pd.DataFrame) -> BaseSampleNormalizer:
+    def fit(self, table: pd.DataFrame) -> Self:
         """Returns the instance itself."""
         return self
 
@@ -440,7 +457,7 @@ class ZscoreScaler(BaseSampleNormalizer):
 
 
 def confirm_is_fitted(
-    normalizer: BaseSampleNormalizer, msg: Optional[str] = None
+    normalizer: AbstractTransformer, msg: Optional[str] = None
 ) -> None:
     """Perform is_fitted validation for normalizer instances.
 

msreport/plot.py

@@ -703,16 +703,18 @@ def volcano_ma(
         y_col = " ".join([y_variable, comparison_group])
         x_values = data[x_col]
         y_values = data[y_col]
-        ax.grid(axis="both", linestyle="dotted", linewidth=1)
+        xy_labels = data[annotation_column]
 
-        mask = masks["default"]
-        ax.scatter(x_values[mask], y_values[mask], **params["default"])
+        valid_values = np.isfinite(x_values) & np.isfinite(y_values)
+        mask_default = masks["default"] & valid_values
+        mask_special = masks["highlight"] & valid_values
 
-        mask = masks["highlight"]
+        ax.grid(axis="both", linestyle="dotted", linewidth=1)
+        ax.scatter(x_values[mask_default], y_values[mask_default], **params["default"])
         _annotated_scatter(
-            x_values=data[x_col][mask],
-            y_values=data[y_col][mask],
-            labels=data[annotation_column][mask],
+            x_values=x_values[mask_special],
+            y_values=y_values[mask_special],
+            labels=xy_labels[mask_special],
             ax=ax,
             scatter_kws=params["highlight"],
         )

{msreport-0.0.26.dist-info → msreport-0.0.27.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: msreport
-Version: 0.0.26
+Version: 0.0.27
 Summary: Post processing and analysis of quantitative proteomics data
 Author-email: "David M. Hollenstein" <hollenstein.david@gmail.com>
 License: Apache-2.0
@@ -24,6 +24,7 @@ Requires-Dist: scikit-learn>=1.0.0
 Requires-Dist: scipy>=1.9.1
 Requires-Dist: seaborn>=0.12.0
 Requires-Dist: statsmodels>=0.13.2
+Requires-Dist: typing_extensions>=4
 Dynamic: license-file
 
 [![Project Status: WIP – Initial development is in progress, but there has not yet been a stable, usable release suitable for the public.](https://www.repostatus.org/badges/latest/wip.svg)](https://www.repostatus.org/#wip)

{msreport-0.0.26.dist-info → msreport-0.0.27.dist-info}/RECORD

@@ -1,13 +1,13 @@
-msreport/__init__.py,sha256=plg-xX45MtHFaMW2qKkNZMTku2gH1Eu5iY4mmFdYSa8,343
-msreport/analyze.py,sha256=JBLuFLYJjI-8NIIwzq2gEJKJYFmKyuLUwf8NgSzC9_c,25350
+msreport/__init__.py,sha256=RPN5o7ubtWIQgnnnG7kAq9pBQzM40dSeeMlr_TYp1n8,343
+msreport/analyze.py,sha256=ihdHqqmaRrCI8NXJP-jUfmvNAtSRUwVU7ixOkpgW9z4,28048
 msreport/errors.py,sha256=qJan3lzRX6uwnByg9LfAfGKEKC2tm9SYUBvk3TdH_AM,300
 msreport/export.py,sha256=pyB8D1VjvfJWO6ka6uMnHsbc6SRlmCyhUB2sfBlhYDQ,20095
 msreport/fasta.py,sha256=oS7n_wNu-4num5nMUiL5cTpMRU3dBe4Xurz09bGm9ZE,1083
-msreport/impute.py,sha256=UJXfni8xjfIrdaq-tIa9MOyklHLQxq-LHRlbHi7G5IM,10441
+msreport/impute.py,sha256=cBFAaMTlzjdG99ABDHtiN6ZcHpddnx5lfqUp-A4Vr3M,10341
 msreport/isobar.py,sha256=H6AJA81AJQ-gGoc8NEFpNAe6ofwzoK4BGnxQHZ80GlA,6551
-msreport/normalize.py,sha256=fQx1QQxusrfddcA_oATz88_ojOqClLQVxNNoJxdOOX4,19334
+msreport/normalize.py,sha256=Dm3loQjNqFWG1D-k5lAhwKzB_2G6ufa4R5cF5gqqYuE,20158
 msreport/peptidoform.py,sha256=C0IWyvnKivGyizkrtpA_i_lLgw8YZgIxuFBtURrE6rw,11879
-msreport/plot.py,sha256=MUWYSzNKRct9JYDQE7uL_zLxlG8vjTS2so9e4EXyvHw,44005
+msreport/plot.py,sha256=gyMCMy5uDuqdGH71wRW_jJdohB5yaWeYbX5jvA0kSWc,44186
 msreport/qtable.py,sha256=g9hrVyUdQbiNkBnnFNp4JXNiEAEb_yddrefy34gYMgM,22947
 msreport/reader.py,sha256=PngSiFqX0uFcXCwyU9lwKANGgG8PeoejpcMB3EmlvQc,104972
 msreport/aggregate/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -15,7 +15,7 @@ msreport/aggregate/condense.py,sha256=sNBEsSqCej-zvzd8QeyaScBxUnP_UcaZWzQx9dvRAD
 msreport/aggregate/pivot.py,sha256=tCxdhSdXAgEobnsp-n2DX91PwTiNYbx_FYgY6SOef4M,5079
 msreport/aggregate/summarize.py,sha256=aI0YP9Kg4ZTVjS6c9gzu3xqvLOTsYJ5ZT3FcUJyg1vk,12155
 msreport/helper/__init__.py,sha256=8B7gdXn5tFeZATBF30TMaWu0ppc7xFa72JLxMYt_qUM,535
-msreport/helper/calc.py,sha256=ReMP1jA7bz-a7J1DdlAVATN9zjSXENqbw652WfjSEkY,4088
+msreport/helper/calc.py,sha256=yZ-mp2V9_XrCf75mpOlmyZV3Q3lVINqROMVp33TXW6A,4246
 msreport/helper/maxlfq.py,sha256=DE9yX4vjMRSmolffrpC9UkCXmSs-rCN15cnlNzma4zw,14938
 msreport/helper/table.py,sha256=N-veDU3vQ2NeOfKcxUop5SfCv2iW038akkSKxU2yjzg,11464
 msreport/helper/temp.py,sha256=jNulgDATf9sKXEFWMXAhjflciOZPAqlxg_7QZS7IkW8,3736
@@ -23,8 +23,8 @@ msreport/rinterface/__init__.py,sha256=Z1I-4buERXTPIZmhdaTKZWfbJv_qVcqnUVqIJZx1D
 msreport/rinterface/limma.py,sha256=ATtsVyGSnqUGkyodQTgdpIFhEb4dJZ6wvSjrRsCrNRY,5421
 msreport/rinterface/rinstaller.py,sha256=sm6CJD0-XSxdDpUnL9EAI_CAIgo1NucYxPI9gL93zqw,1377
 msreport/rinterface/rscripts/limma.R,sha256=gr_yjMm_YoG45irDhWOo6gkRQSTwj_7uU_p3NBRHPm8,4331
-msreport-0.0.26.dist-info/licenses/LICENSE.txt,sha256=Pd-b5cKP4n2tFDpdx27qJSIq0d1ok0oEcGTlbtL6QMU,11560
-msreport-0.0.26.dist-info/METADATA,sha256=0OpBlUdIaAqhdzEK9Mkq12rVJpeJHuYflFI4griTxqE,5339
-msreport-0.0.26.dist-info/WHEEL,sha256=ck4Vq1_RXyvS4Jt6SI0Vz6fyVs4GWg7AINwpsaGEgPE,91
-msreport-0.0.26.dist-info/top_level.txt,sha256=Drl8mCckJHFIw-Ovh5AnyjKnqvLJltDOBUr1JAcHAlI,9
-msreport-0.0.26.dist-info/RECORD,,
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