pilotpy 2.0.2__py3-none-any.whl

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/pl.py

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+from .plot import *

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/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])
+
+