pilotpy 2.0.2__tar.gz

pilotpy-2.0.2/LICENSE

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+MIT License
+
+Copyright (c) 2024 PILOT (https://github.com/CostaLab/PILOT)
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

pilotpy-2.0.2/PKG-INFO

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+Metadata-Version: 2.1
+Name: pilotpy
+Version: 2.0.2
+Summary: PILOT: Detection of PatIent-Level distances from single cell genomics and pathomics data with Optimal Transport (PILOT)
+License: MIT
+Author: Mehdi Joodaki
+Requires-Python: ==3.11.5
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3
+Requires-Dist: POT (>=0.9.3,<0.10.0)
+Requires-Dist: adjustText (>=1.1.1,<2.0.0)
+Requires-Dist: cycler (>=0.12.1,<0.13.0)
+Requires-Dist: elpigraph-python (>=0.3.1,<0.4.0)
+Requires-Dist: gprofiler-official (>=1.0.0,<2.0.0)
+Requires-Dist: joypy (>=0.2.6,<0.3.0)
+Requires-Dist: leidenalg (>=0.10.2,<0.11.0)
+Requires-Dist: matplotlib (>=3.8.4,<4.0.0)
+Requires-Dist: numpy (>=1.26.4,<2.0.0)
+Requires-Dist: pandas (>=2.2.2,<3.0.0)
+Requires-Dist: plotly (>=5.22.0,<6.0.0)
+Requires-Dist: plotnine (>=0.13.5,<0.14.0)
+Requires-Dist: pydiffmap (>=0.2.0.1,<0.3.0.0)
+Requires-Dist: scanpy (>=1.10.1,<2.0.0)
+Requires-Dist: scikit-learn (>=1.4.2,<2.0.0)
+Requires-Dist: scikit-network (>=0.32.1,<0.33.0)
+Requires-Dist: scipy (>=1.13.0,<2.0.0)
+Requires-Dist: seaborn (>=0.13.2,<0.14.0)
+Requires-Dist: shap (>=0.45.0,<0.46.0)
+Requires-Dist: statsmodels (>=0.14.2,<0.15.0)
+Description-Content-Type: text/markdown
+
+# PILOT  <img src="img/logo.png" align="right" width="300" />
+
+[![GitHub license](https://img.shields.io/github/license/CostaLab/PILOT.svg)](https://github.com/CostaLab/PILOT?tab=MIT-1-ov-file#MIT-1-ov-file)
+
+**Authors:**
+ Mehdi Joodaki<sup>[*1]</sup>
+ ,Mina Shaigan<sup>[*1]</sup>
+ ,Victor Parra<sup>[1]</sup>
+ ,Roman D. Bülow<sup>[2]</sup>
+ ,Christoph Kuppe<sup>[3]</sup>
+ ,David L. Hölscher<sup>[2]</sup>
+ ,Mingbo Cheng<sup>[1]</sup>
+ ,James S. Nagai<sup>[1]</sup>
+ ,Michaël Goedertier<sup>[1,2]</sup>
+ ,Nassim Bouteldja<sup>[2]</sup>
+ ,Vladimir Tesar<sup>[5]</sup> 
+,Jonathan Barratt<sup>[6,7]</sup>
+ ,Ian S.D. Roberts<sup>[8]</sup>
+ ,Rosanna Coppo<sup>[9]</sup>
+ ,Rafael Kramann<sup>[3,4]</sup>
+ ,Peter Boor<sup>[2,@]</sup>
+ ,Ivan G. Costa<sup>[1,@]</sup>
+
+**Affiliations:**
+- [1] Institute for Computational Genomics, Joint Research Center for Computational Biomedicine, RWTH Aachen University Medical School
+- [2] Institute of Pathology, Laboratory of Nephropathology, RWTH Aachen University Medical School
+- [3] Institute of Experimental Medicine and Systems Biology, RWTH Aachen University
+- [4] Department of Internal Medicine, Nephrology and Transplantation, Erasmus Medical Center
+- [5] Department of Nephrology, $1^{st}$ Faculty of Medicine and General University Hospital, Charles University, Prague, Czech Republic
+- [6] John Walls Renal Unit, University Hospital of Leicester National Health Service Trust, Leicester, United Kingdom
+- [7] Department of Cardiovascular Sciences, University of Leicester, Leicester, United Kingdom
+- [8] Department of Cellular Pathology, Oxford University Hospitals National Health Services Foundation Trust, Oxford, United Kingdom
+- [9] Fondazione Ricerca Molinette. Regina Margherita Children's University Hospital, Torino, Italy
+  
+![plot](./img/plot.png)
+
+
+Current version for PILOT is 2.0.2
+
+## Installation
+The easiest way to install PILOT and the required packages is using the following way:
+
+```terminal
+git clone https://github.com/CostaLab/PILOT
+cd PILOT
+conda create --name PILOT r-base
+conda activate PILOT
+conda install -c conda-forge rpy2
+conda install jupyter
+pip install .
+```
+Once you've completed these steps, you can proceed to run the tutorials and explore the features of PILOT. 
+When doing so, remember to move to the tutorial folder, as all the work will be performed there:
+
+```terminal
+cd Tutorial
+```
+
+## [Tutorial&Data sets](https://pilot.readthedocs.io/en/latest/index.html)
+There are five tutorials, one for [Myocardial Infarction (single cell data)](https://pilot.readthedocs.io/en/latest/Myocardial_infarction.html), and the second tutorial for [pathomics data, the combination of Kidney IgAN(G) & Kidney IgAN(T)](https://pilot.readthedocs.io/en/latest/Combination_Kidney_IgAN.html), and the third one  for [Patients sub-group detection and then ranking cells/genes (Pancreas data)](https://pilot.readthedocs.io/en/latest/Patients_sub_group_detection.html) and the forth one for 
+[evaluation of the presence of batch effects in Trajectory](https://pilot.readthedocs.io/en/latest/Kidney_trajectory.html) and the last one for [evaluation of the presence of batch effects in detected sub-groups](https://pilot.readthedocs.io/en/latest/Kidney_clusters.html).
+
+
+You can access the used data sets by PILOT in Part 1 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.4740646.svg)](https://zenodo.org/records/8370081) and  Part 2 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.4740646.svg)](https://zenodo.org/records/7957118)
+
+# References
+ PILOT: Detection of PatIent-Level distances from single cell genomics and pathomics data with Optimal Transport (PILOT) [link](https://www.embopress.org/doi/full/10.1038/s44320-023-00003-8)
+
+
+
+
+
+
+
+

pilotpy-2.0.2/README.md

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+# PILOT  <img src="img/logo.png" align="right" width="300" />
+
+[![GitHub license](https://img.shields.io/github/license/CostaLab/PILOT.svg)](https://github.com/CostaLab/PILOT?tab=MIT-1-ov-file#MIT-1-ov-file)
+
+**Authors:**
+ Mehdi Joodaki<sup>[*1]</sup>
+ ,Mina Shaigan<sup>[*1]</sup>
+ ,Victor Parra<sup>[1]</sup>
+ ,Roman D. Bülow<sup>[2]</sup>
+ ,Christoph Kuppe<sup>[3]</sup>
+ ,David L. Hölscher<sup>[2]</sup>
+ ,Mingbo Cheng<sup>[1]</sup>
+ ,James S. Nagai<sup>[1]</sup>
+ ,Michaël Goedertier<sup>[1,2]</sup>
+ ,Nassim Bouteldja<sup>[2]</sup>
+ ,Vladimir Tesar<sup>[5]</sup> 
+,Jonathan Barratt<sup>[6,7]</sup>
+ ,Ian S.D. Roberts<sup>[8]</sup>
+ ,Rosanna Coppo<sup>[9]</sup>
+ ,Rafael Kramann<sup>[3,4]</sup>
+ ,Peter Boor<sup>[2,@]</sup>
+ ,Ivan G. Costa<sup>[1,@]</sup>
+
+**Affiliations:**
+- [1] Institute for Computational Genomics, Joint Research Center for Computational Biomedicine, RWTH Aachen University Medical School
+- [2] Institute of Pathology, Laboratory of Nephropathology, RWTH Aachen University Medical School
+- [3] Institute of Experimental Medicine and Systems Biology, RWTH Aachen University
+- [4] Department of Internal Medicine, Nephrology and Transplantation, Erasmus Medical Center
+- [5] Department of Nephrology, $1^{st}$ Faculty of Medicine and General University Hospital, Charles University, Prague, Czech Republic
+- [6] John Walls Renal Unit, University Hospital of Leicester National Health Service Trust, Leicester, United Kingdom
+- [7] Department of Cardiovascular Sciences, University of Leicester, Leicester, United Kingdom
+- [8] Department of Cellular Pathology, Oxford University Hospitals National Health Services Foundation Trust, Oxford, United Kingdom
+- [9] Fondazione Ricerca Molinette. Regina Margherita Children's University Hospital, Torino, Italy
+  
+![plot](./img/plot.png)
+
+
+Current version for PILOT is 2.0.2
+
+## Installation
+The easiest way to install PILOT and the required packages is using the following way:
+
+```terminal
+git clone https://github.com/CostaLab/PILOT
+cd PILOT
+conda create --name PILOT r-base
+conda activate PILOT
+conda install -c conda-forge rpy2
+conda install jupyter
+pip install .
+```
+Once you've completed these steps, you can proceed to run the tutorials and explore the features of PILOT. 
+When doing so, remember to move to the tutorial folder, as all the work will be performed there:
+
+```terminal
+cd Tutorial
+```
+
+## [Tutorial&Data sets](https://pilot.readthedocs.io/en/latest/index.html)
+There are five tutorials, one for [Myocardial Infarction (single cell data)](https://pilot.readthedocs.io/en/latest/Myocardial_infarction.html), and the second tutorial for [pathomics data, the combination of Kidney IgAN(G) & Kidney IgAN(T)](https://pilot.readthedocs.io/en/latest/Combination_Kidney_IgAN.html), and the third one  for [Patients sub-group detection and then ranking cells/genes (Pancreas data)](https://pilot.readthedocs.io/en/latest/Patients_sub_group_detection.html) and the forth one for 
+[evaluation of the presence of batch effects in Trajectory](https://pilot.readthedocs.io/en/latest/Kidney_trajectory.html) and the last one for [evaluation of the presence of batch effects in detected sub-groups](https://pilot.readthedocs.io/en/latest/Kidney_clusters.html).
+
+
+You can access the used data sets by PILOT in Part 1 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.4740646.svg)](https://zenodo.org/records/8370081) and  Part 2 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.4740646.svg)](https://zenodo.org/records/7957118)
+
+# References
+ PILOT: Detection of PatIent-Level distances from single cell genomics and pathomics data with Optimal Transport (PILOT) [link](https://www.embopress.org/doi/full/10.1038/s44320-023-00003-8)
+
+
+
+
+
+
+

pilotpy-2.0.2/pyproject.toml

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+[tool.poetry]
+name = "pilotpy"
+version = "2.0.2"
+description = "PILOT: Detection of PatIent-Level distances from single cell genomics and pathomics data with Optimal Transport (PILOT)"
+authors = ["Mehdi Joodaki"]
+license = "MIT license"
+readme = "README.md"
+
+[tool.poetry.dependencies]
+python = "3.11.5"
+cycler = "^0.12.1"
+joypy = "^0.2.6"
+leidenalg = "^0.10.2"
+numpy = "^1.26.4"
+matplotlib = "^3.8.4"
+pandas = "^2.2.2"
+plotly = "^5.22.0"
+plotnine = "^0.13.5"
+POT = "^0.9.3"
+pydiffmap = "^0.2.0.1"
+scanpy = "^1.10.1"
+scikit-learn = "^1.4.2"
+scikit-network = "^0.32.1"
+scipy = "^1.13.0"
+seaborn = "^0.13.2"
+shap = "^0.45.0"
+statsmodels = "^0.14.2"
+elpigraph-python = "^0.3.1"
+adjustText = "^1.1.1"
+gprofiler-official = "^1.0.0"
+
+
+[build-system]
+requires = ["poetry-core"]
+build-backend = "poetry.core.masonry.api"

pilotpy-2.0.2/src/pilotpy/__init__.py

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+__version__ = "2.0.2"
+__author__ = 'Mehdi Joodaki'
+__credits__ = 'Institute for Computational Genomics'
+
+from . import tl
+from . import pl

pilotpy-2.0.2/src/pilotpy/pl.py

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+from .plot import *

pilotpy-2.0.2/src/pilotpy/plot/__init__.py

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+from .ploting import *
+from .curve_activity import *
+from .gene_selection_analysis import *
+from .pseudobulk_DE_analysis import *
+

pilotpy-2.0.2/src/pilotpy/plot/curve_activity.py

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+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+# This code had been adapted from https://github.com/pinellolab/dictys
+# Wang, L., Trasanidis, N., Wu, T. et al. Dictys: dynamic gene regulatory 
+## network dissects developmental continuum with single-cell multiomics. 
+### Nat Methods 20, 1368–1378 (2023).
+
+import numpy as np
+
+def auc(curves, times):
+    """
+	Computes area under the curves.
+	Parameters
+	----------
+	times:	numpy.ndarray(shape=(n,))
+		X coordinates
+	curves:	numpy.ndarray(shape=(ny,n))
+		Y coordinates, one for each y curve
+	Returns
+	-------
+	numpy.ndarray(shape=(ny,))
+		Area under the curves
+	"""
+
+    if len(times) < 2 or not (times[1:] > times[:-1]).all():
+        raise ValueError('times must be increasing and have at least 2 values.')
+    timesdiff = times[1:] - times[:-1]
+    curvesmean = (curves[:,1:] + curves[:, :-1]) / 2
+    ans = curvesmean@timesdiff
+    return ans
+
+def _curvesnamic_network_char_terminal_logfc_(curves, times):
+	"""
+	Computes terminal logFC for curves.
+	Parameters
+	----------
+	times:	numpy.ndarray(shape=(n,))
+		X coordinates
+	curves:	numpy.ndarray(shape=(ny,n))
+		Y coordinates, one for each y curve
+	Returns
+	-------
+	numpy.ndarray(shape=(ny,))
+		Terminal logFCs
+	"""
+	if len(times) < 2 or not (times[1:] > times[:-1]).all():
+		raise ValueError('times must be increasing and have at least 2 values.')
+	return (curves[:,-1] - curves[:,0]) / (times[-1] - times[0])
+
+def _curvesnamic_network_char_transient_logfc_(curves, times):
+    """
+	Computes transient logFC for curves.
+	Parameters
+	----------
+	times:	numpy.ndarray(shape=(n,))
+		X coordinates 
+	curves:	numpy.ndarray(shape=(ny,n))
+		Y coordinates, one for each y curve
+	Returns
+	-------
+	numpy.ndarray(shape=(ny,))
+		Transient logFCs
+    """
+    n = curves.shape[1]
+    times = (times - times[0]) / (times[-1] - times[0])
+    curves = curves - np.median([curves, np.repeat(curves[:, [0]], n, axis = 1), np.repeat(curves[:, [-1]], n, axis = 1)], axis = 0)
+    return auc(curves, times)
+
+def _curvesnamic_network_char_switching_time_(curves, times):
+    """
+   	Computes switching time for curves.
+   	Parameters
+   	----------
+   	times:	numpy.ndarray(shape=(n,))
+   		X coordinates
+   	curves:	numpy.ndarray(shape=(ny,n))
+   		Y coordinates, one for each y curve
+   	Returns
+   	-------
+   	numpy.ndarray(shape=(ny,))
+   		Switching time
+    """
+    n = curves.shape[1]
+    times = (times - times[0]) / (times[-1] - times[0])
+    curves = np.median([curves, np.repeat(curves[:, [0]], n, axis = 1), np.repeat(curves[:, [-1]], n, axis = 1)], axis = 0)
+    return (auc((curves.T - curves[:, -1]).T, times)) / (curves[:, 0] - curves[:, -1] + 1E-300)
+
+
+def _curvesnamic_network_char_area_(curves, times):
+    return abs(curves[:, 0] + curves[:, -1]) * abs(times[-1] - times[0])
+
+