msreport 0.0.28__tar.gz → 0.0.30__tar.gz

msreport-0.0.30/PKG-INFO

@@ -0,0 +1,144 @@
+Metadata-Version: 2.4
+Name: msreport
+Version: 0.0.30
+Summary: Post processing and analysis of quantitative proteomics data
+Author-email: "David M. Hollenstein" <hollenstein.david@gmail.com>
+License-Expression: Apache-2.0
+Project-URL: homepage, https://github.com/hollenstein/msreport
+Project-URL: changelog, https://github.com/hollenstein/msreport/blob/main/CHANGELOG.md
+Keywords: mass spectrometry,proteomics,post processing,data analysis
+Classifier: Development Status :: 4 - Beta
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE.txt
+Requires-Dist: adjustText<1.0.0,>=0.7.0
+Requires-Dist: matplotlib>=3.5.2
+Requires-Dist: numpy>=1.21.5
+Requires-Dist: pandas>=1.4.4
+Requires-Dist: profasta>=0.0.4
+Requires-Dist: pyteomics>=4.6.0
+Requires-Dist: pyyaml>=6.0.0
+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
+Provides-Extra: r
+Requires-Dist: rpy2<3.5.13,>=3.5.3; extra == "r"
+Provides-Extra: dev
+Requires-Dist: mypy>=1.15.0; extra == "dev"
+Requires-Dist: pytest>=8.3.5; extra == "dev"
+Provides-Extra: test
+Requires-Dist: pytest>=8.3.5; extra == "test"
+Dynamic: license-file
+
+# MsReport
+
+[![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)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.15309090.svg)](https://doi.org/10.5281/zenodo.15309090)
+![Python Version from PEP 621 TOML](https://img.shields.io/python/required-version-toml?tomlFilePath=https%3A%2F%2Fraw.githubusercontent.com%2Fhollenstein%2Fmsreport%2Fmain%2Fpyproject.toml)
+[![Run tests](https://github.com/hollenstein/msreport/actions/workflows/run-tests.yml/badge.svg)](https://github.com/hollenstein/msreport/actions/workflows/run-tests.yml)
+
+**MsReport** is a Python library for post-processing quantitative proteomics data from
+bottom-up mass spectrometry experiments.
+
+## Table of Contents
+
+- [What is MsReport?](#what-is-msreport)
+  - [Key features of MsReport](#key-features-of-msreport)
+- [Installation](#installation)
+    - [Installation when using Anaconda](#installation-when-using-anaconda)
+    - [Additional requirements](#additional-requirements)
+    - [Optional Dependencies](#optional-dependencies)
+- [Development status](#development-status)
+- [How to cite](#how-to-cite)
+
+## What is MsReport?
+
+MsReport is a Python library designed to simplify the post-processing and analysis of quantitative proteomics data from bottom-up mass spectrometry experiments. It provides a high-level, abstraction-focused API for efficient and standardized workflows. The modular design of the library provides the flexibility to meet project specific data processing needs and customize workflows as required.
+
+The library supports importing protein and peptide-level quantification results from MaxQuant, FragPipe, and Spectronaut, as well as post-translational modification (PTM) data from MaxQuant and FragPipe. MsReport provides tools for data annotation, normalization and transformation, statistical testing, and data visualization.
+
+### Key features of MsReport
+
+#### Data Import and Standardization
+
+The `reader` module provides software-specific reader classes for importing data from MaxQuant, FragPipe, and Spectronaut that enable the import of protein, peptide and ion tables. During the import process, these classes transform tables column names and table values into a standardized format to ensure that the rest of the library can operate in a tool-agnostic manner.
+
+#### Data management
+
+The `qtable` module provides a structured approach to managing quantitative data through its central `Qtable` class. This class combines quantitative data with an experimental design table that defines the relationship between samples and experimental conditions. The quantitative data is stored in a wide format, where each sample's measurements are stored in separate columns. The `Qtable` class serves as the foundation for data analysis workflows in MsReport, providing the standardized data structure used by the `analyze`, `plot`, and `export` modules.
+
+#### Data processing and analysis
+
+The `analyze` module provides tools for post-processing of mass spectrometry data generated by software such as MaxQuant, FragPipe, or Spectronaut. It includes functions for filtering, normalization, imputation of missing values, and statistical testing. The library integrates with the R package LIMMA to enable differential expression analysis.
+
+> [!NOTE]  
+> In order to use the R integration you need to install msreport with optional dependencies, see [Optional Dependencies](#optional-dependencies) for more information.
+
+#### Data visualization
+
+The `plot` module supports the generation of visualizations for quality control and data analysis. It includes functions for creating various plots, such as intensity and ratio distributions, heatmaps, volcano plots, and PCA plots.
+
+#### Data export
+
+Finally, the `export` module enables the conversion and export into formats compatible with external tools. This includes generating input files for [Amica](https://bioapps.maxperutzlabs.ac.at/app/amica) and exporting tables for easier integration with Perseus. 
+
+## Installation
+
+If you do not already have a Python installation, we recommend installing the [Anaconda distribution](https://www.anaconda.com/download) or [Miniconda](https://docs.anaconda.com/free/miniconda/index.html) distribution from Continuum Analytics, which already contains a large number of popular Python packages for Data Science. Alternatively, you can also get Python from the [Python homepage](https://www.python.org/downloads/windows). Note that MsReport requires Python version 3.10 or higher.
+
+The following command will install MsReport and its dependencies by using a wheel file.
+
+```shell
+pip install msreport
+```
+
+To uninstall the MsReport library use:
+
+```shell
+pip uninstall msreport
+```
+
+### Installation when using Anaconda
+
+To install the MsReport library using Anaconda, you need to either activate a custom conda environment or install it into the default base environment. Open the Anaconda Navigator, activate the desired conda environment or use the base environment, and then open a command line by running the "CMD.exe" application. Finally, use the `pip install` command as before.
+
+### Optional Dependencies
+
+#### R Integration
+
+MsReport provides an interface to the R package LIMMA for differential expression analysis. To use this functionality, you need:
+
+- A local installation of **R (version 4.0 or higher)**.
+- The system environment variable R_HOME set to the R home directory.
+- To install msreport with the optional dependencies for R integration.
+
+```shell
+pip install msreport[R]
+```
+
+#### Setting the R_HOME environment variable
+
+On Windows, you may need to restart your computer after modifying the system environment variables for the changes to take effect. To find the R home directory, you can run the following command in R:
+
+```R
+normalizePath(R.home("home"))
+```
+
+For example, the R home directory might look like this on Windows: `C:\Program Files\R\R-4.2.1`
+
+## Development status
+
+MsReport is a stable and reliable library that has been used on a daily basis for over two years in the Mass Spectrometry Facility at the Max Perutz Labs and the Mass Spectrometry Facility of IMP/IMBA/GMI. While the current interface of MsReport is stable, the library is still under active development, with new features being added regularly. Please note that a major rewrite is planned, which may introduce changes to the API in the future.
+
+## How to cite
+
+If you use MsReport for your research or publications, please include the following citation and consider giving the project a star on GitHub.
+
+> Hollenstein, D. M., & Hartl, M. (2025). hollenstein/msreport: v0.0.29 (0.0.29). Zenodo. https://doi.org/10.5281/zenodo.15309090

msreport-0.0.30/README.md

@@ -0,0 +1,105 @@
+# MsReport
+
+[![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)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.15309090.svg)](https://doi.org/10.5281/zenodo.15309090)
+![Python Version from PEP 621 TOML](https://img.shields.io/python/required-version-toml?tomlFilePath=https%3A%2F%2Fraw.githubusercontent.com%2Fhollenstein%2Fmsreport%2Fmain%2Fpyproject.toml)
+[![Run tests](https://github.com/hollenstein/msreport/actions/workflows/run-tests.yml/badge.svg)](https://github.com/hollenstein/msreport/actions/workflows/run-tests.yml)
+
+**MsReport** is a Python library for post-processing quantitative proteomics data from
+bottom-up mass spectrometry experiments.
+
+## Table of Contents
+
+- [What is MsReport?](#what-is-msreport)
+  - [Key features of MsReport](#key-features-of-msreport)
+- [Installation](#installation)
+    - [Installation when using Anaconda](#installation-when-using-anaconda)
+    - [Additional requirements](#additional-requirements)
+    - [Optional Dependencies](#optional-dependencies)
+- [Development status](#development-status)
+- [How to cite](#how-to-cite)
+
+## What is MsReport?
+
+MsReport is a Python library designed to simplify the post-processing and analysis of quantitative proteomics data from bottom-up mass spectrometry experiments. It provides a high-level, abstraction-focused API for efficient and standardized workflows. The modular design of the library provides the flexibility to meet project specific data processing needs and customize workflows as required.
+
+The library supports importing protein and peptide-level quantification results from MaxQuant, FragPipe, and Spectronaut, as well as post-translational modification (PTM) data from MaxQuant and FragPipe. MsReport provides tools for data annotation, normalization and transformation, statistical testing, and data visualization.
+
+### Key features of MsReport
+
+#### Data Import and Standardization
+
+The `reader` module provides software-specific reader classes for importing data from MaxQuant, FragPipe, and Spectronaut that enable the import of protein, peptide and ion tables. During the import process, these classes transform tables column names and table values into a standardized format to ensure that the rest of the library can operate in a tool-agnostic manner.
+
+#### Data management
+
+The `qtable` module provides a structured approach to managing quantitative data through its central `Qtable` class. This class combines quantitative data with an experimental design table that defines the relationship between samples and experimental conditions. The quantitative data is stored in a wide format, where each sample's measurements are stored in separate columns. The `Qtable` class serves as the foundation for data analysis workflows in MsReport, providing the standardized data structure used by the `analyze`, `plot`, and `export` modules.
+
+#### Data processing and analysis
+
+The `analyze` module provides tools for post-processing of mass spectrometry data generated by software such as MaxQuant, FragPipe, or Spectronaut. It includes functions for filtering, normalization, imputation of missing values, and statistical testing. The library integrates with the R package LIMMA to enable differential expression analysis.
+
+> [!NOTE]  
+> In order to use the R integration you need to install msreport with optional dependencies, see [Optional Dependencies](#optional-dependencies) for more information.
+
+#### Data visualization
+
+The `plot` module supports the generation of visualizations for quality control and data analysis. It includes functions for creating various plots, such as intensity and ratio distributions, heatmaps, volcano plots, and PCA plots.
+
+#### Data export
+
+Finally, the `export` module enables the conversion and export into formats compatible with external tools. This includes generating input files for [Amica](https://bioapps.maxperutzlabs.ac.at/app/amica) and exporting tables for easier integration with Perseus. 
+
+## Installation
+
+If you do not already have a Python installation, we recommend installing the [Anaconda distribution](https://www.anaconda.com/download) or [Miniconda](https://docs.anaconda.com/free/miniconda/index.html) distribution from Continuum Analytics, which already contains a large number of popular Python packages for Data Science. Alternatively, you can also get Python from the [Python homepage](https://www.python.org/downloads/windows). Note that MsReport requires Python version 3.10 or higher.
+
+The following command will install MsReport and its dependencies by using a wheel file.
+
+```shell
+pip install msreport
+```
+
+To uninstall the MsReport library use:
+
+```shell
+pip uninstall msreport
+```
+
+### Installation when using Anaconda
+
+To install the MsReport library using Anaconda, you need to either activate a custom conda environment or install it into the default base environment. Open the Anaconda Navigator, activate the desired conda environment or use the base environment, and then open a command line by running the "CMD.exe" application. Finally, use the `pip install` command as before.
+
+### Optional Dependencies
+
+#### R Integration
+
+MsReport provides an interface to the R package LIMMA for differential expression analysis. To use this functionality, you need:
+
+- A local installation of **R (version 4.0 or higher)**.
+- The system environment variable R_HOME set to the R home directory.
+- To install msreport with the optional dependencies for R integration.
+
+```shell
+pip install msreport[R]
+```
+
+#### Setting the R_HOME environment variable
+
+On Windows, you may need to restart your computer after modifying the system environment variables for the changes to take effect. To find the R home directory, you can run the following command in R:
+
+```R
+normalizePath(R.home("home"))
+```
+
+For example, the R home directory might look like this on Windows: `C:\Program Files\R\R-4.2.1`
+
+## Development status
+
+MsReport is a stable and reliable library that has been used on a daily basis for over two years in the Mass Spectrometry Facility at the Max Perutz Labs and the Mass Spectrometry Facility of IMP/IMBA/GMI. While the current interface of MsReport is stable, the library is still under active development, with new features being added regularly. Please note that a major rewrite is planned, which may introduce changes to the API in the future.
+
+## How to cite
+
+If you use MsReport for your research or publications, please include the following citation and consider giving the project a star on GitHub.
+
+> Hollenstein, D. M., & Hartl, M. (2025). hollenstein/msreport: v0.0.29 (0.0.29). Zenodo. https://doi.org/10.5281/zenodo.15309090

{msreport-0.0.28 → msreport-0.0.30}/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__ = "0.0.28"
+__version__ = "0.0.30"

{msreport-0.0.28 → msreport-0.0.30}/msreport/analyze.py

@@ -9,10 +9,19 @@ import numpy as np
 import pandas as pd
 
 import msreport.normalize
-import msreport.rinterface
+from msreport.errors import OptionalDependencyError
 from msreport.helper import find_sample_columns
 from msreport.qtable import Qtable
 
+try:
+    import msreport.rinterface
+
+    _rinterface_available = True
+    _rinterface_error = ""
+except OptionalDependencyError as err:
+    _rinterface_available = False
+    _rinterface_error = str(err)
+
 
 class Transformer(Protocol):
     def fit(self, table: pd.DataFrame) -> Transformer:
@@ -528,8 +537,10 @@ def calculate_multi_group_limma(
         ValueError: If all values from qtable.design["Batch"] are identical when 'batch'
             is set to True.
     """
-    _validate_experiment_pairs(qtable, experiment_pairs)
+    if not _rinterface_available:
+        raise OptionalDependencyError(_rinterface_error)
 
+    _validate_experiment_pairs(qtable, experiment_pairs)
     # TODO: not tested #
     if batch and "Batch" not in qtable.get_design():
         raise KeyError(
@@ -618,8 +629,10 @@ def calculate_two_group_limma(
             must have exactly two entries and the two entries must not be the same. Both
             experiments must be present in qtable.design.
     """
-    _validate_experiment_pair(qtable, experiment_pair)
+    if not _rinterface_available:
+        raise OptionalDependencyError(_rinterface_error)
 
+    _validate_experiment_pair(qtable, experiment_pair)
     # TODO: LIMMA function not tested #
     table = qtable.make_expression_table(samples_as_columns=True)
     comparison_tag = " vs "

{msreport-0.0.28 → msreport-0.0.30}/msreport/errors.py

@@ -7,3 +7,7 @@ class NotFittedError(ValueError, AttributeError):
 
 class ProteinsNotInFastaWarning(UserWarning):
     """Warning raised when queried proteins are absent from a FASTA file."""
+
+
+class OptionalDependencyError(ImportError):
+    """Raised when an optional dependency is required but not installed."""

{msreport-0.0.28 → msreport-0.0.30}/msreport/plot/distribution.py

@@ -204,7 +204,8 @@ def experiment_ratios(
     mask = np.all([(qtable.data[f"Events {exp}"] > 0) for exp in experiments], axis=0)
     if exclude_invalid:
         mask = mask & qtable["Valid"]
-    experiment_data = experiment_data[mask]
+    # Use `mask.to_numpy` to solve issue with different indices of mask and dataframe
+    experiment_data = experiment_data[mask.to_numpy()]
     pseudo_reference = np.nanmean(experiment_data, axis=1)
     ratio_data = experiment_data.subtract(pseudo_reference, axis=0)
 

{msreport-0.0.28 → msreport-0.0.30}/msreport/qtable.py

@@ -27,13 +27,11 @@ class Qtable:
         design: A pandas.DataFrame describing the experimental design.
     """
 
-    _default_id_column = "Representative protein"
-
     def __init__(
         self,
         data: pd.DataFrame,
-        design: Optional[pd.DataFrame] = None,
-        id_column: str = "Representative protein",
+        design: pd.DataFrame,
+        id_column: str,
     ):
         """Initializes the Qtable.
 
@@ -42,12 +40,13 @@ class Qtable:
 
         Args:
             data: A dataframe containing quantitative proteomics data in a wide format.
+                The index of the dataframe must contain unique values.
             design: A dataframe describing the experimental design that must at least
                 contain the columns "Sample" and "Experiment". The "Sample" entries
                 should correspond to the Sample names present in the quantitative
                 columns of the data.
             id_column: The name of the column that contains the unique identifiers for
-                the entries in the data table. Default is "Representative protein".
+                the entries in the data table.
 
         Raises:
             KeyError: If the specified id_column is not found in data.
@@ -76,8 +75,7 @@ class Qtable:
         self._id_column = id_column
         if "Valid" not in self.data.columns:
             self.data["Valid"] = True
-        if design is not None:
-            self.add_design(design)
+        self.add_design(design)
 
         self._expression_columns: list[str] = []
         self._expression_features: list[str] = []
@@ -438,6 +436,11 @@ class Qtable:
 
         Returns:
             An instance of Qtable loaded from the specified files.
+
+        Raises:
+            ValueError: If the loaded config file does not contain the
+                "Unique ID column" key. This is due to the qtable being saved with a
+                version of msreport <= 0.0.27.
         """
         filepaths = _get_qtable_export_filepaths(directory, basename)
         with open(filepaths["config"]) as openfile:
@@ -458,13 +461,20 @@ class Qtable:
                 filepaths["design"], sep="\t", index_col=0, keep_default_na=True
             )
 
-        qtable = Qtable(data, design)
+        if "Unique ID column" not in config_data:
+            # Mention that the qtable was likely saved with a version of msreport <= 0.0.27
+            raise ValueError(
+                "The qtable config file does not contain the 'Unique ID column' key. "
+                "This is likely due to the qtable being saved with a version of "
+                "msreport <= 0.0.27."
+            )
+        id_column = config_data["Unique ID column"]
+
+        qtable = Qtable(data, design, id_column)
         qtable._expression_columns = config_data["Expression columns"]
         qtable._expression_features = config_data["Expression features"]
         qtable._expression_sample_mapping = config_data["Expression sample mapping"]
         # This check is required for backwards compatibility with msreport <= 0.0.27
-        if "Unique ID column" in config_data:
-            qtable._id_column = config_data["Unique ID column"]
         return qtable
 
     def to_tsv(self, path: str, index: bool = False):
@@ -570,7 +580,7 @@ class Qtable:
         self._expression_sample_mapping = {}
 
     def __copy__(self) -> Qtable:
-        new_instance = Qtable(self.data, self.design)
+        new_instance = Qtable(self.data, self.design, self.id_column)
         # Copy all private attributes
         for attr in dir(self):
             if (