acore 0.1.0__tar.gz

acore-0.1.0/AUTHORS.rst

@@ -0,0 +1,13 @@
+=======
+Credits
+=======
+
+Development Lead
+----------------
+
+* Alberto Santos Delgado <albsad@dtu.dk>
+
+Contributors
+------------
+
+None yet. Why not be the first?

acore-0.1.0/CONTRIBUTING.rst

@@ -0,0 +1,128 @@
+.. highlight:: shell
+
+============
+Contributing
+============
+
+Contributions are welcome, and they are greatly appreciated! Every little bit
+helps, and credit will always be given.
+
+You can contribute in many ways:
+
+Types of Contributions
+----------------------
+
+Report Bugs
+~~~~~~~~~~~
+
+Report bugs at https://github.com/albsantosdel/acore/issues.
+
+If you are reporting a bug, please include:
+
+* Your operating system name and version.
+* Any details about your local setup that might be helpful in troubleshooting.
+* Detailed steps to reproduce the bug.
+
+Fix Bugs
+~~~~~~~~
+
+Look through the GitHub issues for bugs. Anything tagged with "bug" and "help
+wanted" is open to whoever wants to implement it.
+
+Implement Features
+~~~~~~~~~~~~~~~~~~
+
+Look through the GitHub issues for features. Anything tagged with "enhancement"
+and "help wanted" is open to whoever wants to implement it.
+
+Write Documentation
+~~~~~~~~~~~~~~~~~~~
+
+acore could always use more documentation, whether as part of the
+official acore docs, in docstrings, or even on the web in blog posts,
+articles, and such.
+
+Submit Feedback
+~~~~~~~~~~~~~~~
+
+The best way to send feedback is to file an issue at https://github.com/albsantosdel/acore/issues.
+
+If you are proposing a feature:
+
+* Explain in detail how it would work.
+* Keep the scope as narrow as possible, to make it easier to implement.
+* Remember that this is a volunteer-driven project, and that contributions
+  are welcome :)
+
+Get Started!
+------------
+
+Ready to contribute? Here's how to set up `acore` for local development.
+
+1. Fork the `acore` repo on GitHub.
+2. Clone your fork locally::
+
+    $ git clone git@github.com:your_name_here/acore.git
+
+3. Install your local copy into a virtualenv. Assuming you have virtualenvwrapper installed, this is how you set up your fork for local development::
+
+    $ mkvirtualenv acore
+    $ cd acore/
+    $ python setup.py develop
+
+4. Create a branch for local development::
+
+    $ git checkout -b name-of-your-bugfix-or-feature
+
+   Now you can make your changes locally.
+
+5. When you're done making changes, check that your changes pass flake8 and the
+   tests, including testing other Python versions with tox::
+
+    $ flake8 acore tests
+    $ python setup.py test or pytest
+    $ tox
+
+   To get flake8 and tox, just pip install them into your virtualenv.
+
+6. Commit your changes and push your branch to GitHub::
+
+    $ git add .
+    $ git commit -m "Your detailed description of your changes."
+    $ git push origin name-of-your-bugfix-or-feature
+
+7. Submit a pull request through the GitHub website.
+
+Pull Request Guidelines
+-----------------------
+
+Before you submit a pull request, check that it meets these guidelines:
+
+1. The pull request should include tests.
+2. If the pull request adds functionality, the docs should be updated. Put
+   your new functionality into a function with a docstring, and add the
+   feature to the list in README.rst.
+3. The pull request should work for Python 3.5, 3.6, 3.7 and 3.8, and for PyPy. Check
+   https://travis-ci.com/albsantosdel/acore/pull_requests
+   and make sure that the tests pass for all supported Python versions.
+
+Tips
+----
+
+To run a subset of tests::
+
+$ pytest tests.test_acore
+
+
+Deploying
+---------
+
+A reminder for the maintainers on how to deploy.
+Make sure all your changes are committed (including an entry in HISTORY.rst).
+Then run::
+
+$ bump2version patch # possible: major / minor / patch
+$ git push
+$ git push --tags
+
+Travis will then deploy to PyPI if tests pass.

acore-0.1.0/HISTORY.rst

@@ -0,0 +1,8 @@
+=======
+History
+=======
+
+0.1.0 (2023-09-26)
+------------------
+
+* First release on PyPI.

acore-0.1.0/LICENSE

@@ -0,0 +1,33 @@
+GNU GENERAL PUBLIC LICENSE
+                      Version 3, 29 June 2007
+
+    A Python package with statistical functions to analyse multimodal molecular data
+    Copyright (C) 2023  Alberto Santos Delgado
+
+    This program is free software: you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+
+    This program is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+Also add information on how to contact you by electronic and paper mail.
+
+  You should also get your employer (if you work as a programmer) or school,
+if any, to sign a "copyright disclaimer" for the program, if necessary.
+For more information on this, and how to apply and follow the GNU GPL, see
+<http://www.gnu.org/licenses/>.
+
+  The GNU General Public License does not permit incorporating your program
+into proprietary programs.  If your program is a subroutine library, you
+may consider it more useful to permit linking proprietary applications with
+the library.  If this is what you want to do, use the GNU Lesser General
+Public License instead of this License.  But first, please read
+<http://www.gnu.org/philosophy/why-not-lgpl.html>.
+

acore-0.1.0/MANIFEST.in

@@ -0,0 +1,11 @@
+include AUTHORS.rst
+include CONTRIBUTING.rst
+include HISTORY.rst
+include LICENSE
+include README.rst
+
+recursive-include tests *
+recursive-exclude * __pycache__
+recursive-exclude * *.py[co]
+
+recursive-include docs *.rst conf.py Makefile make.bat *.jpg *.png *.gif

acore-0.1.0/PKG-INFO

@@ -0,0 +1,112 @@
+Metadata-Version: 2.1
+Name: acore
+Version: 0.1.0
+Summary: A Python package with statistical functions to analyse multimodal molecular data
+Home-page: https://github.com/Multiomics-Analytics-Group/acore
+Author-email: Alberto Santos Delgado <albsad@dtu.dk>
+License: GNU General Public License v3
+Project-URL: Homepage, https://github.com/Multiomics-Analytics-Group/acore
+Project-URL: Issues, https://github.com/Multiomics-Analytics-Group/acore/issues
+Project-URL: Documentation, https://analytics-core.readthedocs.io/
+Classifier: Development Status :: 2 - Pre-Alpha
+Classifier: Intended Audience :: Developers
+Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
+Classifier: Natural Language :: English
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Requires-Python: >=3.6
+Description-Content-Type: text/x-rst
+License-File: LICENSE
+License-File: AUTHORS.rst
+Requires-Dist: click>=7.0
+Requires-Dist: numpy==1.23.2
+Requires-Dist: pandas==2.0.2
+Requires-Dist: scipy==1.10.1
+Requires-Dist: networkx==3.1
+Requires-Dist: biopython==1.81
+Requires-Dist: combat==0.3.3
+Requires-Dist: gseapy==1.0.4
+Requires-Dist: kmapper==2.0.1
+Requires-Dist: lifelines==0.27.7
+Requires-Dist: pingouin==0.5.3
+Requires-Dist: python-louvain==0.16
+Requires-Dist: PyWGCNA==1.16.8
+Requires-Dist: snfpy==0.2.2
+Requires-Dist: umap-learn==0.5.3
+Requires-Dist: statsmodels
+Provides-Extra: dev
+Requires-Dist: pytest>=3; extra == "dev"
+
+==============
+Analytics Core
+==============
+
+
+.. start-badges
+
+.. list-table::
+    :stub-columns: 1
+
+    * - docs
+      - |docs|
+    * - tests
+      - | |Pylint|
+    * - package
+      - | |version| |wheel| |supported-versions| |supported-implementations|
+      
+.. |docs| image:: https://readthedocs.org/projects/acore/badge/?style=flat
+    :target: https://analytics-core.readthedocs.io/
+    :alt: Documentation Status
+
+.. |Pylint| image:: https://github.com/Multiomics-Analytics-Group/acore/actions/workflows/tox-gha.yml/badge.svg
+    :alt: GitHub Actions Tox Status
+    :target: https://github.com/Multiomics-Analytics-Group/acore/actions/workflows/tox.yml
+
+.. |version| image:: https://img.shields.io/pypi/v/acore.svg
+    :alt: PyPI Package latest release
+    :target: https://pypi.org/project/acore
+
+.. |wheel| image:: https://img.shields.io/pypi/wheel/acore.svg
+    :alt: PyPI Wheel
+    :target: https://pypi.org/project/acore
+
+.. |supported-versions| image:: https://img.shields.io/pypi/pyversions/acore.svg
+    :alt: Supported versions
+    :target: https://pypi.org/project/acore
+
+.. |supported-implementations| image:: https://img.shields.io/pypi/implementation/acore.svg
+    :alt: Supported implementations
+    :target: https://pypi.org/project/acore
+
+.. end-badges
+
+
+
+
+A Python package with statistical functions to analyse multimodal molecular data
+
+
+* Free software: GNU General Public License v3
+* Documentation: https://analytics-core.readthedocs.io.
+
+
+Installation
+============
+
+::
+
+    pip install acore
+
+You can also install the in-development version with::
+
+    pip install https://github.com/Multiomics-Analytics-Group/acore/archive/main.zip
+
+
+
+Development
+===========
+
+To run all the tests run::
+
+    pytest 

acore-0.1.0/README.rst

@@ -0,0 +1,72 @@
+==============
+Analytics Core
+==============
+
+
+.. start-badges
+
+.. list-table::
+    :stub-columns: 1
+
+    * - docs
+      - |docs|
+    * - tests
+      - | |Pylint|
+    * - package
+      - | |version| |wheel| |supported-versions| |supported-implementations|
+      
+.. |docs| image:: https://readthedocs.org/projects/acore/badge/?style=flat
+    :target: https://analytics-core.readthedocs.io/
+    :alt: Documentation Status
+
+.. |Pylint| image:: https://github.com/Multiomics-Analytics-Group/acore/actions/workflows/tox-gha.yml/badge.svg
+    :alt: GitHub Actions Tox Status
+    :target: https://github.com/Multiomics-Analytics-Group/acore/actions/workflows/tox.yml
+
+.. |version| image:: https://img.shields.io/pypi/v/acore.svg
+    :alt: PyPI Package latest release
+    :target: https://pypi.org/project/acore
+
+.. |wheel| image:: https://img.shields.io/pypi/wheel/acore.svg
+    :alt: PyPI Wheel
+    :target: https://pypi.org/project/acore
+
+.. |supported-versions| image:: https://img.shields.io/pypi/pyversions/acore.svg
+    :alt: Supported versions
+    :target: https://pypi.org/project/acore
+
+.. |supported-implementations| image:: https://img.shields.io/pypi/implementation/acore.svg
+    :alt: Supported implementations
+    :target: https://pypi.org/project/acore
+
+.. end-badges
+
+
+
+
+A Python package with statistical functions to analyse multimodal molecular data
+
+
+* Free software: GNU General Public License v3
+* Documentation: https://analytics-core.readthedocs.io.
+
+
+Installation
+============
+
+::
+
+    pip install acore
+
+You can also install the in-development version with::
+
+    pip install https://github.com/Multiomics-Analytics-Group/acore/archive/main.zip
+
+
+
+Development
+===========
+
+To run all the tests run::
+
+    pytest 

acore-0.1.0/acore/__init__.py

@@ -0,0 +1 @@
+__version__ = "0.1.0"

acore-0.1.0/acore/correlation_analysis.py

@@ -0,0 +1,194 @@
+import itertools
+import numpy as np
+import pandas as pd
+from scipy import stats
+import pingouin as pg
+from scipy.special import betainc
+import acore.utils as utils
+from acore.multiple_testing import apply_pvalue_correction
+
+
+def calculate_correlations(x, y, method='pearson'):
+    """
+    Calculates a Spearman (nonparametric) or a Pearson (parametric) correlation coefficient and p-value to test for non-correlation.
+
+    :param ndarray x: array 1
+    :param ndarray y: array 2
+    :param str method: chooses which kind of correlation method to run
+    :return: Tuple with two floats, correlation coefficient and two-tailed p-value.
+
+    Example::
+
+        result = calculate_correlations(x, y, method='pearson')
+    """
+    if method == "pearson":
+        coefficient, pvalue = stats.pearsonr(x, y)
+    elif method == "spearman":
+        coefficient, pvalue = stats.spearmanr(x, y)
+
+    return (coefficient, pvalue)
+
+
+def run_correlation(df, alpha=0.05, subject='subject', group='group', method='pearson', correction='fdr_bh'):
+    """
+    This function calculates pairwise correlations for columns in dataframe, and returns it in the shape of a edge list with 'weight' as correlation score, and the ajusted p-values.
+
+    :param df: pandas dataframe with samples as rows and features as columns.
+    :param str subject: name of column containing subject identifiers.
+    :param str group: name of column containing group identifiers.
+    :param str method: method to use for correlation calculation ('pearson', 'spearman').
+    :param floar alpha: error rate. Values velow alpha are considered significant.
+    :param string correction: type of correction see apply_pvalue_correction for methods
+    :return: Pandas dataframe with columns: 'node1', 'node2', 'weight', 'padj' and 'rejected'.
+
+    Example::
+
+        result = run_correlation(df, alpha=0.05, subject='subject', group='group', method='pearson', correction='fdr_bh')
+    """
+    correlation = pd.DataFrame()
+    # ToDo
+    # The Repeated measurements correlation calculation is too time consuming so it only runs if
+    # the number of features is less than 200
+    if utils.check_is_paired(df, subject, group):
+        if len(df[subject].unique()) > 2:
+            if len(df.columns) < 200:
+                correlation = run_rm_correlation(df, alpha=alpha, subject=subject, correction=correction)
+    else:
+        df = df.dropna(axis=1)._get_numeric_data()
+        if not df.empty:
+            r, p = run_efficient_correlation(df, method=method)
+            rdf = pd.DataFrame(r, index=df.columns, columns=df.columns)
+            pdf = pd.DataFrame(p, index=df.columns, columns=df.columns)
+            correlation = utils.convertToEdgeList(rdf, ["node1", "node2", "weight"])
+            pvalues = utils.convertToEdgeList(pdf, ["node1", "node2", "pvalue"])
+            correlation = pd.merge(correlation, pvalues, on=['node1', 'node2'])
+
+            rejected, padj = apply_pvalue_correction(correlation["pvalue"].tolist(), alpha=alpha, method=correction)
+            correlation["padj"] = padj
+            correlation["rejected"] = rejected
+            correlation = correlation[correlation.rejected]
+            correlation["pvalue"] = correlation["pvalue"].apply(lambda x: str(round(x, 5)))
+            correlation["padj"] = correlation["padj"].apply(lambda x: str(round(x, 5)))
+
+    return correlation
+
+
+def run_multi_correlation(df_dict, alpha=0.05, subject='subject', on=['subject', 'biological_sample'], group='group', method='pearson', correction='fdr_bh'):
+    """
+    This function merges all input dataframes and calculates pairwise correlations for all columns.
+
+    :param dict df_dict: dictionary of pandas dataframes with samples as rows and features as columns.
+    :param str subject: name of the column containing subject identifiers.
+    :param str group: name of the column containing group identifiers.
+    :param list on: column names to join dataframes on (must be found in all dataframes).
+    :param str method: method to use for correlation calculation ('pearson', 'spearman').
+    :param float alpha: error rate. Values velow alpha are considered significant.
+    :param string correction: type of correction see apply_pvalue_correction for methods
+    :return: Pandas dataframe with columns: 'node1', 'node2', 'weight', 'padj' and 'rejected'.
+
+    Example::
+
+        result = run_multi_correlation(df_dict, alpha=0.05, subject='subject', on=['subject', 'biological_sample'] , group='group', method='pearson', correction='fdr_bh')
+    """
+    multidf = pd.DataFrame()
+    correlation = None
+    for dtype in df_dict:
+        if multidf.empty:
+            if isinstance(df_dict[dtype], pd.DataFrame):
+                multidf = df_dict[dtype]
+        else:
+            if isinstance(df_dict[dtype], pd.DataFrame):
+                multidf = pd.merge(multidf, df_dict[dtype], how='inner', on=on)
+    if not multidf.empty:
+        correlation = run_correlation(multidf, alpha=alpha, subject=subject, group=group, method=method, correction=correction)
+
+    return correlation
+
+
+def calculate_rm_correlation(df, x, y, subject):
+    """
+    Computes correlation and p-values between two columns a and b in df.
+
+    :param df: pandas dataframe with subjects as rows and two features and columns.
+    :param str x: feature a name.
+    :param str y: feature b name.
+    :param subject: column name containing the covariate variable.
+    :return: Tuple with values for: feature a, feature b, correlation, p-value and degrees of freedom.
+
+    Example::
+
+        result = calculate_rm_correlation(df, x='feature a', y='feature b', subject='subject')
+    """
+    result = pg.rm_corr(data=df, x=x, y=y, subject=subject)
+
+    return (x, y, result["r"].values[0], result["pval"].values[0], result["dof"].values[0])
+
+
+def run_rm_correlation(df, alpha=0.05, subject='subject', correction='fdr_bh'):
+    """
+    Computes pairwise repeated measurements correlations for all columns in dataframe, and returns results as an edge list with 'weight' as correlation score, p-values, degrees of freedom and ajusted p-values.
+
+    :param df: pandas dataframe with samples as rows and features as columns.
+    :param str subject: name of column containing subject identifiers.
+    :param float alpha: error rate. Values velow alpha are considered significant.
+    :param string correction: type of correction type see apply_pvalue_correction for methods
+    :return: Pandas dataframe with columns: 'node1', 'node2', 'weight', 'pvalue', 'dof', 'padj' and 'rejected'.
+
+    Example::
+
+        result = run_rm_correlation(df, alpha=0.05, subject='subject', correction='fdr_bh')
+    """
+    rows = []
+    if not df.empty:
+        df = df.set_index(subject)._get_numeric_data().dropna(axis=1)
+        df.columns = df.columns.astype(str)
+        combinations = itertools.combinations(df.columns, 2)
+        df = df.reset_index()
+        for x, y in combinations:
+            row = [x, y]
+            subset = df[[x, y, subject]]
+            row.extend(pg.rm_corr(subset, x, y, subject).values.tolist()[0])
+            rows.append(row)
+
+        correlation = pd.DataFrame(rows, columns=["node1", "node2", "weight", "dof", "pvalue", "CI95%", "power"])
+        rejected, padj = apply_pvalue_correction(correlation["pvalue"].tolist(), alpha=alpha, method=correction)
+        correlation["padj"] = padj
+        correlation["rejected"] = rejected
+        correlation = correlation[correlation.rejected]
+        correlation["padj"] = correlation["padj"].apply(lambda x: str(round(x, 5)))
+
+    return correlation
+
+
+def run_efficient_correlation(data, method='pearson'):
+    """
+    Calculates pairwise correlations and returns lower triangle of the matrix with correlation values and p-values.
+
+    :param data: pandas dataframe with samples as index and features as columns (numeric data only).
+    :param str method: method to use for correlation calculation ('pearson', 'spearman').
+    :return: Two numpy arrays: correlation and p-values.
+
+    Example::
+
+        result = run_efficient_correlation(data, method='pearson')
+    """
+    matrix = data.values
+    if method == 'pearson':
+        r = np.corrcoef(matrix, rowvar=False)
+    elif method == 'spearman':
+        r, p = stats.spearmanr(matrix, axis=0)
+
+    diagonal = np.triu_indices(r.shape[0], 1)
+    rf = r[diagonal]
+    df = matrix.shape[1] - 2
+    ts = rf * rf * (df / (1 - rf * rf))
+    pf = betainc(0.5 * df, 0.5, df / (df + ts))
+    p = np.zeros(shape=r.shape)
+    p[np.triu_indices(p.shape[0], 1)] = pf
+    p[np.tril_indices(p.shape[0], -1)] = pf
+    p[np.diag_indices(p.shape[0])] = np.ones(p.shape[0])
+
+    r[diagonal] = np.nan
+    p[diagonal] = np.nan
+
+    return r, p