msreport 0.0.24__tar.gz

msreport-0.0.24/LICENSE.txt

@@ -0,0 +1,202 @@
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msreport-0.0.24/PKG-INFO

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+Metadata-Version: 2.4
+Name: msreport
+Version: 0.0.24
+Summary: Post processing and analysis of quantitative proteomics data
+Author-email: "David M. Hollenstein" <hollenstein.david@gmail.com>
+License: Apache-2.0
+Keywords: mass spectrometry,proteomics,post processing,data analysis
+Classifier: Development Status :: 3 - Alpha
+Classifier: License :: OSI Approved :: Apache Software License
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Python: >=3.9
+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: rpy2>=3.5.3
+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
+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
+
+
+## Introduction
+
+MsReport is a python library that allows simple and standardized post processing of
+quantitative proteomics data from bottom up, mass spectrometry experiments. Currently
+working with label free protein quantification reports from MaxQuant and FragPipe is
+fully supported. Other data analysis pipelines can be added by writing a software
+specific reader function.
+
+MsReport is primarily developed as a tool for the Mass Spectrometry Facility at the Max
+Perutz Labs (University of Vienna), to allow the generation of Quantitative Protein and
+PTM reports, and to facilitate project specific data analysis tasks.
+
+
+## Release
+
+Development is currently in early alpha and the interface is not yet stable.
+
+
+## Scope
+
+The `reader` module contains software specific reader classes that provide access to the
+outputs of the respective software. Reader instances allow importing protein and ion
+tables, and provide the ability to standardize column names and data formats during the
+import. To do so, reader classes must know the file structure and naming conventions of
+the respective software.
+
+The `qtable` class allows storing and accessing quantitative data from a particular
+level of abstraction, such as proteins or ions, and an experimental design table that
+describes to which experiment a sample belongs to. The quantitative data are in the wide
+format, i.e. the quantification data of each sample is stored in a separate column. The
+`Qtable` allows convenient handling and access to quantitative data through information
+from the experimental design, and represents the data structure used by the `analyze`,
+`plot`, and `export` modules.
+
+The `analyze` module provides a high-level interface for post-processing of quantitative
+data, such as filtering valid values, normalization between samples, imputation of
+missing values, and statistical testing with the R package LIMMA.
+
+The `plot` module allows generation of quality control and data analysis plots.
+
+Using methods from the `export` module allows conversion and export of quantitative data
+into the Amica input format, and generating contaminant tables for the inspection of
+potential contaminants.
+
+Additional scripts
+
+- The `excel_report` module enables the creation of a formatted excel protein report
+  by using the XlsxReport library.
+- The `benchmark` module contains functions to generate benchmark plots from multiple
+  `Qtable` instances, and can be used for method or software comparison.
+
+
+## Install
+
+If you do not already have a Python installation, we recommend installing the
+[Anaconda distribution](https://www.continuum.io/downloads) of 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). MsReport requires Python
+version 3.9 or higher.
+
+You can use pip to install MsReport from the distribution file with the following
+command:
+
+```
+pip install msreport-X.Y.Z-py3-none-any.whl
+```
+
+To uninstall the MsReport library type:
+
+```
+pip uninstall msreport
+```
+
+
+### Installation when using Anaconda
+If you are using Anaconda, you will need to install the MsReport package into a conda
+environment. Open the Anaconda navigator, activate the conda environment you want to
+use, run the "CMD.exe" application to open a terminal, and then use the pip install
+command as described above.
+
+
+### Additional requirements
+
+MsReport provides an interface to the R package LIMMA for differential expression
+analysis, which requires a local installation of R (R version 3.4 or higher) and the
+system environment variable "R_HOME" to be set to the R home directory. Note that it
+might be necessary to restart the computer after adding the "R_HOME" variable. The R
+home directory can also be found from within R by using the command below, and might
+look similar to "C:\Program Files\R\R-4.2.1" on windows.
+
+```
+normalizePath(R.home("home"))
+```

msreport-0.0.24/README.md

@@ -0,0 +1,100 @@
+[![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
+
+
+## Introduction
+
+MsReport is a python library that allows simple and standardized post processing of
+quantitative proteomics data from bottom up, mass spectrometry experiments. Currently
+working with label free protein quantification reports from MaxQuant and FragPipe is
+fully supported. Other data analysis pipelines can be added by writing a software
+specific reader function.
+
+MsReport is primarily developed as a tool for the Mass Spectrometry Facility at the Max
+Perutz Labs (University of Vienna), to allow the generation of Quantitative Protein and
+PTM reports, and to facilitate project specific data analysis tasks.
+
+
+## Release
+
+Development is currently in early alpha and the interface is not yet stable.
+
+
+## Scope
+
+The `reader` module contains software specific reader classes that provide access to the
+outputs of the respective software. Reader instances allow importing protein and ion
+tables, and provide the ability to standardize column names and data formats during the
+import. To do so, reader classes must know the file structure and naming conventions of
+the respective software.
+
+The `qtable` class allows storing and accessing quantitative data from a particular
+level of abstraction, such as proteins or ions, and an experimental design table that
+describes to which experiment a sample belongs to. The quantitative data are in the wide
+format, i.e. the quantification data of each sample is stored in a separate column. The
+`Qtable` allows convenient handling and access to quantitative data through information
+from the experimental design, and represents the data structure used by the `analyze`,
+`plot`, and `export` modules.
+
+The `analyze` module provides a high-level interface for post-processing of quantitative
+data, such as filtering valid values, normalization between samples, imputation of
+missing values, and statistical testing with the R package LIMMA.
+
+The `plot` module allows generation of quality control and data analysis plots.
+
+Using methods from the `export` module allows conversion and export of quantitative data
+into the Amica input format, and generating contaminant tables for the inspection of
+potential contaminants.
+
+Additional scripts
+
+- The `excel_report` module enables the creation of a formatted excel protein report
+  by using the XlsxReport library.
+- The `benchmark` module contains functions to generate benchmark plots from multiple
+  `Qtable` instances, and can be used for method or software comparison.
+
+
+## Install
+
+If you do not already have a Python installation, we recommend installing the
+[Anaconda distribution](https://www.continuum.io/downloads) of 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). MsReport requires Python
+version 3.9 or higher.
+
+You can use pip to install MsReport from the distribution file with the following
+command:
+
+```
+pip install msreport-X.Y.Z-py3-none-any.whl
+```
+
+To uninstall the MsReport library type:
+
+```
+pip uninstall msreport
+```
+
+
+### Installation when using Anaconda
+If you are using Anaconda, you will need to install the MsReport package into a conda
+environment. Open the Anaconda navigator, activate the conda environment you want to
+use, run the "CMD.exe" application to open a terminal, and then use the pip install
+command as described above.
+
+
+### Additional requirements
+
+MsReport provides an interface to the R package LIMMA for differential expression
+analysis, which requires a local installation of R (R version 3.4 or higher) and the
+system environment variable "R_HOME" to be set to the R home directory. Note that it
+might be necessary to restart the computer after adding the "R_HOME" variable. The R
+home directory can also be found from within R by using the command below, and might
+look similar to "C:\Program Files\R\R-4.2.1" on windows.
+
+```
+normalizePath(R.home("home"))
+```

msreport-0.0.24/msreport/__init__.py

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+from msreport.qtable import Qtable
+from msreport.reader import MaxQuantReader, FragPipeReader, SpectronautReader
+
+from msreport.fasta import import_protein_database
+
+import msreport.analyze
+import msreport.export
+import msreport.impute
+import msreport.normalize
+import msreport.plot
+import msreport.reader
+
+__version__ = "0.0.24"

msreport-0.0.24/msreport/aggregate/condense.py

@@ -0,0 +1,163 @@
+import numpy as np
+
+import msreport.helper.maxlfq as MAXLFQ
+
+
+def join_str(array: np.ndarray, sep: str = ";") -> str:
+    """Returns a joined string of sorted values from the array.
+
+    Note that empty strings or np.nan are not included in the joined string.
+    """
+    elements = []
+    for value in array.flatten():
+        if value != "" and not (isinstance(value, float) and np.isnan(value)):
+            elements.append(str(value))
+    return sep.join(sorted(elements))
+
+
+def join_str_per_column(array: np.ndarray, sep: str = ";") -> np.ndarray:
+    """Returns for each column a joined string of sorted values.
+
+    Note that empty strings or np.nan are not included in the joined string.
+    """
+    return np.array([join_str(i) for i in array.transpose()])
+
+
+def join_unique_str(array: np.ndarray, sep: str = ";") -> str:
+    """Returns a joined string of unique sorted values from the array."""
+    elements = []
+    for value in array.flatten():
+        if value != "" and not (isinstance(value, float) and np.isnan(value)):
+            elements.append(str(value))
+    return sep.join(sorted(set(elements)))
+
+
+def join_unique_str_per_column(array: np.ndarray, sep: str = ";") -> np.ndarray:
+    """Returns for each column a joined strings of unique sorted values."""
+    return np.array([join_unique_str(i) for i in array.transpose()])
+
+
+def sum(array: np.ndarray) -> float:
+    """Returns sum of values from one or multiple columns.
+
+    Note that if no finite values are present in the array np.nan is returned.
+    """
+    array = array.flatten()
+    if np.isfinite(array).any():
+        return np.nansum(array)
+    else:
+        return np.nan
+
+
+def sum_per_column(array: np.ndarray) -> np.ndarray:
+    """Returns for each column the sum of values.
+
+    Note that if no finite values are present in a column np.nan is returned.
+    """
+    return np.array([sum(i) for i in array.transpose()])
+
+
+def maximum(array: np.ndarray) -> float:
+    """Returns the highest finitevalue from one or multiple columns."""
+    array = array.flatten()
+    if np.isfinite(array).any():
+        return np.nanmax(array)
+    else:
+        return np.nan
+
+
+def maximum_per_column(array: np.ndarray) -> np.ndarray:
+    """Returns for each column the highest finite value."""
+    return np.array([maximum(i) for i in array.transpose()])
+
+
+def minimum(array: np.ndarray) -> int:
+    """Returns the lowest finite value from one or multiple columns."""
+    array = array.flatten()
+    if np.isfinite(array).any():
+        return np.nanmin(array)
+    else:
+        return np.nan
+
+
+def minimum_per_column(array: np.ndarray) -> np.ndarray:
+    """Returns for each column the lowest finite value."""
+    return np.array([minimum(i) for i in array.transpose()])
+
+
+def count_unique(array: np.ndarray) -> int:
+    """Returns the number of unique values from one or multiple columns.
+
+    Note that empty strings or np.nan are not counted as unique values.
+    """
+    unique_elements = {
+        x for x in array.flatten() if not (isinstance(x, float) and np.isnan(x))
+    }
+    unique_elements.discard("")
+
+    return len(unique_elements)
+
+
+def count_unique_per_column(array: np.ndarray) -> np.ndarray:
+    """Returns for each column the number of unique values.
+
+    Note that empty strings or np.nan are not counted as unique values.
+    """
+    if array.size > 0:
+        return np.array([count_unique(i) for i in array.transpose()])
+    else:
+        return np.full(array.shape[0], 0)
+
+
+def profile_by_median_ratio_regression(array: np.ndarray) -> np.ndarray:
+    """Calculates abundance profiles by lstsq regression of pair-wise median ratios.
+
+    The function performs a least squares regression of pair-wise median ratios to
+    calculate estimated abundance profiles.
+
+    Args:
+        array: A two-dimensional array containing abundance values, with the first
+            dimension corresponding to rows and the second dimension to columns.
+            Abundance values must not be log transformed.
+
+    Returns:
+        An array containing estimated abundance profiles, with length equal to the
+        number of columns in the input array.
+    """
+    ratio_matrix = MAXLFQ.calculate_pairwise_median_log_ratio_matrix(
+        array, log_transformed=False
+    )
+    coef_matrix, ratio_array, initial_rows = MAXLFQ.prepare_coefficient_matrix(
+        ratio_matrix
+    )
+    log_profile = MAXLFQ.log_profiles_by_lstsq(coef_matrix, ratio_array)
+    profile = np.power(2, log_profile)
+    return profile
+
+
+def sum_by_median_ratio_regression(array: np.ndarray) -> np.ndarray:
+    """Calculates summed abundance by lstsq regression of pair-wise median ratios.
+
+    The function performs a least squares regression of pair-wise median ratios to
+    calculate estimated abundance profiles. These profiles are then scaled based on the
+    input array such that the columns with finite profile values are used and the sum of
+    the scaled profiles matches the sum of the input array.
+
+    Args:
+        array: A two-dimensional array containing abundance values, with the first
+            dimension corresponding to rows and the second dimension to columns.
+            Abundance values must not be log transformed.
+
+    Returns:
+        An array containing summed abundance estimates, with length equal to the number
+        of columns in the input array.
+    """
+    profile = profile_by_median_ratio_regression(array)
+    scaled_profile = profile
+    if np.isfinite(profile).any():
+        profile_mask = np.isfinite(profile)
+        scaled_profile[profile_mask] = profile[profile_mask] * (
+            np.nansum(array[:, profile_mask]) / np.nansum(profile[profile_mask])
+        )
+
+    return scaled_profile