NetAnalyzer 1.1.0__tar.gz → 1.1.2__tar.gz

{netanalyzer-1.1.0 → netanalyzer-1.1.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: NetAnalyzer
-Version: 1.1.0
+Version: 1.1.2
 Summary: Python package for network analysis, operations and priorization.
 Home-page: https://github.com/seoanezonjic/NetAnalyzer/
 Author: seoanezonjic
@@ -15,7 +15,7 @@ License-File: LICENSE.txt
 Requires-Dist: importlib-metadata; python_version < "3.8"
 Requires-Dist: NetworkX
 Requires-Dist: numpy
-Requires-Dist: scipy==1.13.1
+Requires-Dist: scipy
 Requires-Dist: statsmodels
 Requires-Dist: graphviz
 Requires-Dist: mako
@@ -25,7 +25,7 @@ Requires-Dist: scikit-learn
 Requires-Dist: py_semtools
 Requires-Dist: umap-learn
 Requires-Dist: py_report_html
-Requires-Dist: gensim==4.3.3
+Requires-Dist: gensim
 Requires-Dist: pecanpy
 Requires-Dist: typing_extensions
 Requires-Dist: py_cmdtabs
@@ -33,6 +33,7 @@ Requires-Dist: py_exp_calc
 Requires-Dist: clusim
 Requires-Dist: nodevectors
 Requires-Dist: torch
+Requires-Dist: bicm
 Provides-Extra: testing
 Requires-Dist: setuptools; extra == "testing"
 Requires-Dist: pytest; extra == "testing"
@@ -88,3 +89,5 @@ This package is designed to perform various steps in network analysis and proces
 * Net plotting: Provides several tools for graphing networks from different net plotter packages (igraph, cytoscape, graphviz).
 
 Please, cite this library as: Rojano E., Seoane-Zonjic P., Bueno-Amorós A., Perkins JR., and Ranea JAG. Revealing the Relationship Between Human Genome Regions and Pathological Phenotypes Through Network Analysis. Lecture Notes in Computer Science, DOI: 10.1007/978-3-319-56148-6_17.
+
+See https://github.com/seoanezonjic/NetAnalyzer

{netanalyzer-1.1.0 → netanalyzer-1.1.2}/README.rst

@@ -46,4 +46,6 @@ This package is designed to perform various steps in network analysis and proces
 * Prioritization: Applies propagation algorithms to prioritize nodes based on similarity metrics, such as the adjacency matrix, and a set of seed nodes.
 * Net plotting: Provides several tools for graphing networks from different net plotter packages (igraph, cytoscape, graphviz).
 
-Please, cite this library as: Rojano E., Seoane-Zonjic P., Bueno-Amorós A., Perkins JR., and Ranea JAG. Revealing the Relationship Between Human Genome Regions and Pathological Phenotypes Through Network Analysis. Lecture Notes in Computer Science, DOI: 10.1007/978-3-319-56148-6_17.
+Please, cite this library as: Rojano E., Seoane-Zonjic P., Bueno-Amorós A., Perkins JR., and Ranea JAG. Revealing the Relationship Between Human Genome Regions and Pathological Phenotypes Through Network Analysis. Lecture Notes in Computer Science, DOI: 10.1007/978-3-319-56148-6_17.
+
+See https://github.com/seoanezonjic/NetAnalyzer

{netanalyzer-1.1.0 → netanalyzer-1.1.2}/setup.cfg

@@ -25,7 +25,7 @@ install_requires =
 	importlib-metadata; python_version<"3.8"
 	NetworkX
 	numpy
-	scipy==1.13.1 #Version specified to be compatible with gensim (it allows a version lower than 1.14)
+	scipy #==1.13.1 Version specified to be compatible with gensim (it allows a version lower than 1.14)
 	statsmodels
 	graphviz
 	mako
@@ -35,7 +35,7 @@ install_requires =
 	py_semtools
 	umap-learn
 	py_report_html
-	gensim==4.3.3 #Forcing to this version because it solves "triu" function importing error (it allows to be imported both from numpy and scipy)
+	gensim #==4.3.3 Forcing to this version because it solves "triu" function importing error (it allows to be imported both from numpy and scipy)
 	pecanpy
 	typing_extensions
 	py_cmdtabs
@@ -43,6 +43,7 @@ install_requires =
 	clusim
 	nodevectors
 	torch
+	bicm
 
 [options.packages.find]
 where = src

netanalyzer-1.1.2/src/NetAnalyzer/__init__.py

@@ -0,0 +1,16 @@
+import sys
+
+if sys.version_info[:2] >= (3, 8):
+    # TODO: Import directly (no need for conditional) when `python_requires = >= 3.8`
+    from importlib.metadata import PackageNotFoundError, version  # pragma: no cover
+else:
+    from importlib_metadata import PackageNotFoundError, version  # pragma: no cover
+
+try:
+    # Change here if project is renamed and does not equal the package name
+    dist_name = __name__
+    __version__ = version(dist_name)
+except PackageNotFoundError:  # pragma: no cover
+    __version__ = "unknown"
+finally:
+    del version, PackageNotFoundError

netanalyzer-1.1.2/src/NetAnalyzer/adv_mat_calc.py

@@ -0,0 +1,99 @@
+import warnings
+
+import numpy as np
+class Adv_mat_calc:
+
+	# Alaimo 2014, doi: 10.3389/fbioe.2014.00071
+	@staticmethod
+	def tranference_resources(matrix1, matrix2, lambda_value1 = 0.5, lambda_value2 = 0.5): #2exp?
+		# TODO (Fede,19/12/22) An extension to n layers would be possible with an iterative process.
+		m1rowNumber, m1colNumber = matrix1.shape
+		m2rowNumber, m2colNumber = matrix2.shape
+		matrix1Weight = Adv_mat_calc.graphWeights(m1colNumber, m1rowNumber, matrix1.T, lambda_value1)
+		matrix2Weight = Adv_mat_calc.graphWeights(m2colNumber, m2rowNumber, matrix2.T, lambda_value2)
+		matrixWeightProduct = np.dot(matrix1Weight, np.dot(matrix2, matrix2Weight))
+		finalMatrix = np.dot(matrix1, matrixWeightProduct)
+		return finalMatrix
+
+	@staticmethod
+	def graphWeights(rowsNumber, colsNumber, inputMatrix, lambdaValue = 0.5): #2exp?
+		ky = np.diag((1.0 / inputMatrix.sum(0))) #sum cols
+		weigth = np.dot(inputMatrix, ky).T
+		weigth[np.isnan(weigth)] = 0 # if there is no neighbors, there is no weight
+		ky = None #free memory
+		weigth = np.dot(inputMatrix, weigth)
+
+		kx = inputMatrix.sum(1) #sum rows
+
+		kx_lamb = kx ** lambdaValue
+		kx_lamb_mat = np.zeros((rowsNumber, rowsNumber))
+		for j in range(0,rowsNumber):
+			for i in range(0,rowsNumber):
+				kx_lamb_mat[j,i] = kx_lamb[i]
+		kx_lamb = None #free memory
+
+		kx_inv_lamb = kx ** (1 - lambdaValue)
+		kx_inv_lamb_mat = np.zeros((rowsNumber, rowsNumber))
+		for j in range(0,rowsNumber):
+			for i in range(0,rowsNumber):
+				kx_inv_lamb_mat[j,i] = kx_inv_lamb[i]
+		kx_inv_lamb = None #free memory
+
+		nx = 1.0/(kx_lamb_mat * kx_inv_lamb_mat) # inplace marks a matrix to be used by reference, not for value
+		nx[nx == np.inf] = 0 # if there is no neighbors, there is no weight
+		kx_lamb_mat = None #free memory
+		kx_inv_lamb_mat = None #free memory
+		weigth = weigth * nx
+		return weigth
+
+
+	@staticmethod
+	def disparity_filter_mat(matrix, rowIds, colIds, pval_threshold = 0.05): #2exp?
+		pval_mat = Adv_mat_calc.get_disparity_backbone_pval(matrix)
+		result_mat = pval_mat < pval_threshold
+		new_adj = result_mat.transpose() + result_mat # adjacency matrix, obtained when p[i,j] OR p[j,i] match the criteria
+		matrix[~new_adj] = 0
+
+		# remove nodes with no significance
+		k = np.sum(result_mat, axis=1)
+		final_adj_mat = matrix[:,k>0]
+		final_adj_mat = final_adj_mat[k>0,:]
+		final_rowIds = [node_id for node_id, is_good in zip(rowIds, list(k>0)) if is_good]
+		final_colIds = [node_id for node_id, is_good in zip(colIds, list(k>0)) if is_good]
+
+		return final_adj_mat, final_rowIds, final_colIds
+
+	@staticmethod
+	def filter_rowcols_by_whitelist(matrix, rowIds, colIds, whitelist, symmetric = False): #2exp?
+		row_index = [ i for i, rowId in enumerate(rowIds) if rowId in whitelist ]
+		if symmetric:
+			col_index = row_index
+		else:
+			col_index = [ i for i, colId in enumerate(colIds) if colId in whitelist ]
+		matrix = matrix[row_index]
+		matrix = matrix[:,col_index]
+		rowIds = [rowIds[i] for i in row_index]
+		colIds = [colIds[i] for i in col_index]
+		return matrix, rowIds, colIds
+
+
+	@staticmethod
+	def get_disparity_backbone_pval(matrix): #2exp?
+		# by the moment, implementetion square (?)
+		# TODO: Add a warning when not square matrix.
+		if np.any(matrix < 0):
+			warnings.warn("Negative values detected in matrix. Passing to positive values by subtracting the minimum.")
+			matrix = matrix - np.min(matrix)
+		
+		# row_maxs = np.max(matrix, axis=1, keepdims=True)
+    	# # Avoid division by zero if a row is all zeros
+		# row_maxs[row_maxs == 0] = 1.0 
+		# matrix = matrix / row_maxs
+		W = np.sum(matrix, axis=0)
+		k = (matrix > 0).sum(0)
+		# operacion vectorizada.
+		#
+		pval_mat = np.ones(matrix.shape)
+		for i in range(0,pval_mat.shape[1]):
+			pval_mat[i, :] = (1 - matrix[i, :] / W[i])**(k[i] - 1)
+		return pval_mat

{netanalyzer-1.1.0 → netanalyzer-1.1.2}/src/NetAnalyzer/cli_manager.py

@@ -1,12 +1,12 @@
-import argparse
-import os
-from py_cmdtabs.cmdtabs import CmdTabs
+import argparse, os
 from NetAnalyzer.main_modules import *
 
 ## TYPES 
 def based_0(string): return int(string) - 1
 
-def list_based_0(string): return CmdTabs.parse_column_indices(",", string)
+def list_based_0(string): 
+    from py_cmdtabs.cmdtabs import CmdTabs
+    return CmdTabs.parse_column_indices(",", string)
 
 def single_split(string, sep = ","):
     return string.strip().split(sep)
@@ -182,12 +182,8 @@ def netanalyzer(args=None):
     help="select association method to perform the projections: counts, jaccard, simpson, geometric, cosine, pcc, hypergeometric, hypergeometric_bf, hypergeometric_bh, csi, transference, correlation, umap, pca, bicm")
     parser.add_argument("-a","--assoc_file", dest="assoc_file", default='assoc_values.txt',
     help="Output file name for association values")
-    parser.add_argument("-p","--performance_file", dest="performance_file", default='perf_values.txt',
-    help="Output file name for performance values")
     parser.add_argument("-u","--use_layers", dest="use_layers", default=[['layer']], type= lambda x: double_split(x, sep1=";",sep2=","),
     help="Set which layers must be used on association methods: layer1,layer2;layerA,layerB")
-    parser.add_argument("-c","--control_file", dest="control_file", default=None,
-    help="Control file name")
     # Kernel 
     parser.add_argument("-k","--kernel_method", dest="kernel", default=None,
     help="Kernel operation to perform with the adjacency matrix")
@@ -366,6 +362,8 @@ def text2binary_matrix(args=None):
     parser.add_argument('--sparse_type', dest="sparse_type", default=None, help="""The type of sparse matrix for the output, this option is useful when output type is 
          set to bin. The options are: bsr, coo, csc, csr, dia, dok, lil""")
     parser.add_argument("--round", dest="round", default=None, type=int, help="choose this to round in the i-th digit for all the values in the matrix or relations")
+    parser.add_argument("--filter_by_nodes", dest="filter_by_nodes", default=None, 
+                        help= "File with the list of nodes to take into account in the output matrix, if not set all nodes are included")
     # normalize matrix
     parser.add_argument("--normalize_by", dest="normalize_by", default=None, type=str, help="Type of normalization for matrix: cosine, rows_cols, min_max")
     # order
@@ -373,10 +371,15 @@ def text2binary_matrix(args=None):
             help='File with ROW names to use as index to build the matrix. Order is take into account')
     parser.add_argument('--matrix_col_index', dest="colids_index", default=None,
             help='File with COLUMN names to use as index to build the matrix. Order is take into account')
-    parser.add_argument('--init_matrix_type', dest="init_matrix_type", default="dense",
-            help='Select this to specify which is the matrix type during the intitialization of the matrix. Possible values: dense or an sparse type of scipy (bsr, coo, csc, csr, dia, dok, lil).')
-    parser.add_argument('--output_matrix_type', dest="output_matrix_type", default="dense",
-            help='Select this to specify which is the matrix type during the intitialization of the matrix. Possible values: dense or an sparse type of scipy (bsr, coo, csc, csr, dia, dok, lil).')
+    parser.add_argument('--loading_matrix_format', dest="loading_matrix_format", default="dense",
+            help="""Select this to specify which is the matrix type during the INITIALIZATION of the matrix.
+              Possible values: dense or an sparse type of scipy (bsr, coo, csc, csr, dia, dok, lil).""")
+    parser.add_argument('--output_matrix_format', dest="output_matrix_format", default="dense",
+            help='Select this to specify which is the matrix type during the MANIPULATION of the matrix.' \
+            ' Possible values: dense or an sparse type of scipy (bsr, coo, csc, csr, dia, dok, lil).')
+    parser.add_argument('--write_matrix_format', dest="write_matrix_format", default="dense",
+            help="""Select this to specify which is the matrix type during the WRITING of the matrix.
+              Possible values: dense or an sparse type of scipy (bsr, coo, csc, csr, dia, dok, lil).""")
     opts = parser.parse_args(args)
     main_text2binary_matrix(opts)
 

{netanalyzer-1.1.0 → netanalyzer-1.1.2}/src/NetAnalyzer/graph2sim.py

@@ -1,4 +1,4 @@
-import sys 
+import sys, random 
 import numpy as np
 from scipy import linalg
 from warnings import warn
@@ -9,14 +9,12 @@ import numba #To control pecanpy threading
 from numba import njit, set_num_threads
 from gensim.models import Word2Vec
 import nodevectors
-import random # for the random walker
 
 import torch
 import torch.nn as nn
 import torch.nn.functional as F
 import torch.optim as optim
 import networkx as nx
-import os
 
 
 class LINE(nn.Module):

{netanalyzer-1.1.0 → netanalyzer-1.1.2}/src/NetAnalyzer/integration.py

@@ -1,10 +1,6 @@
-import sys
-import os
-import glob
-import numpy as np
+import itertools, logging
 import concurrent.futures
-import itertools
-import logging
+import numpy as np
 
 class Kernels:
 

{netanalyzer-1.1.0 → netanalyzer-1.1.2}/src/NetAnalyzer/main_modules.py

@@ -1,26 +1,19 @@
-import sys
-import os
-import warnings
+import sys, os, random, copy
 import numpy as np
-import random
-import copy
-from multiprocessing import Process, Manager, Lock
-from py_cmdtabs.cmdtabs import CmdTabs
+import networkx as nx
 import py_exp_calc.exp_calc as pxc
-from py_report_html import Py_report_html
-from NetAnalyzer import Net_parser, NetAnalyzer
-from NetAnalyzer import Kernels
-from NetAnalyzer import Ranker
+from NetAnalyzer.net_parser import Net_parser
+from NetAnalyzer.ranker import Ranker
 #from NetAnalyzer import Graph2sim
-from NetAnalyzer import Adv_mat_calc
-from NetAnalyzer.performancer import Performancer
-from NetAnalyzer.seed_parser import SeedParser
-import networkx as nx
 
 def main_net_explorer(options, test = False):
+    from py_report_html.py_report_html import Py_report_html
     # loading gene seeds.
     options = vars(options)
-    if options["seed_nodes"]: seeds2explore, _ = SeedParser.load_nodes_by_group(options["seed_nodes"], sep=options["seed_sep"])
+    seeds2explore = {"seed": []}
+    if options["seed_nodes"]:
+        from NetAnalyzer.seed_parser import SeedParser 
+        seeds2explore, _ = SeedParser.load_nodes_by_group(options["seed_nodes"], sep=options["seed_sep"])
     if options["group_nodes"]: 
         groups2explore = load_clusters(options)
     else:
@@ -45,23 +38,23 @@ def main_net_explorer(options, test = False):
             multinet[net_id].adjMat2netObj('layer','layer')
 
     # extract a subgraph for each
-    if options["seed_nodes"]:
-        seeds2subgraph = {}
-        seeds2lcc = {}
-        for seed, nodes in seeds2explore.items():
-            seeds2subgraph[seed] = {}
-            seeds2lcc[seed] = {}
-            for net_id, net in multinet.items():
-                # get neighbor from node
-                nodes_with_neigh = set(nodes)
-                if options["neigh_level"].get(net_id):
-                    neigh_level = int(options["neigh_level"].get(net_id))
-                    for i in range(0, neigh_level): nodes_with_neigh = get_neigh_set(net, nodes_with_neigh)
-                    seeds2subgraph[seed][net_id] = net.graph.subgraph(nodes_with_neigh)
-                else:
-                    seeds2subgraph[seed][net_id] = net.graph
-                largest_cc = len(max(nx.connected_components(seeds2subgraph[seed][net_id]), key=len))
-                seeds2lcc[seed][net_id] = largest_cc
+    seeds2lcc = {}
+    seeds2subgraph = {}
+    for seed, nodes in seeds2explore.items():
+        seeds2subgraph[seed] = {}
+        seeds2lcc[seed] = {}
+        for net_id, net in multinet.items():
+            # get neighbor from node
+            nodes_with_neigh = set(nodes) if nodes else set()
+            if options["neigh_level"].get(net_id):
+                neigh_level = int(options["neigh_level"].get(net_id))
+                for i in range(0, neigh_level): nodes_with_neigh = get_neigh_set(net, nodes_with_neigh)
+                seeds2subgraph[seed][net_id] = net.graph.subgraph(nodes_with_neigh)
+            else:
+                seeds2subgraph[seed][net_id] = net.graph
+            largest_cc = len(max(nx.connected_components(seeds2subgraph[seed][net_id]), key=len))
+            seeds2lcc[seed][net_id] = largest_cc
+
 
     # # If mention, add node2vec coordinates with a tnse proyection.
     net2embedding_proj = None
@@ -116,6 +109,7 @@ def get_neigh_set(net, nodes):
 
 
 def main_embedding_integrator(options):
+    from NetAnalyzer.integration import Kernels
     kernels = Kernels()
 
     if not options.kernel_ids:
@@ -143,6 +137,7 @@ def main_embedding_integrator(options):
                 f.write(name + "\n")  
 
 def main_netanalyzer(options):
+    from NetAnalyzer.netanalyzer import NetAnalyzer
     print("Loading network data")
     opts = vars(options)
     # FRED: Remove this part of vars and modify the loads methods (Tlk wth PSZ)
@@ -157,6 +152,7 @@ def main_netanalyzer(options):
         fullNet.ontologies
 
     if options.delete_nodes:
+        from py_cmdtabs.cmdtabs import CmdTabs
         node_list = CmdTabs.load_input_data(options.delete_nodes[0])
         node_list = [item for sublist in node_list for item in sublist]
         mode = options.delete_nodes[1] if len(options.delete_nodes) > 1 else 'd'
@@ -201,18 +197,6 @@ def main_netanalyzer(options):
                 "\t".join(map(str, fullNet.association_values[options.meth][-1])))
         print(f"End of analysis: {options.meth}")
 
-        if options.control_file != None:
-            with open(options.control_file, "r") as f:
-                control = [control.append(line.rstrip().split("\t")) for line in f]
-            Performancer.load_control(control)
-            predictions = fullNet.association_values[options.meth]
-            performance = Performancer.get_pred_rec(predictions)
-            with open(options.performance_file, 'r') as f:
-                f.write("\t".join(['cut', 'prec', 'rec', 'meth']) + "\n")
-                for item in performance:
-                    item.append(options['meth'])
-                    f.write("\t".join(item) + "\n")
-
     if options.kernel or options.external_embedding:
         # This allows inject custom arguments for each embedding method
         embedding_kwargs = eval('{' +options.embedding_add_options +'}')
@@ -436,7 +420,7 @@ def load_kernel(ranker, opts):
         ranker.filter_matrix(opts["whitelist"])
         ranker.clean_seeds()
 
-def sort_records_by_load(records):
+def sort_records_by_load(records, chunk_size):
     recs = []
     slices = int(chunk_size/2)
     r = chunk_size % 2
@@ -446,6 +430,7 @@ def sort_records_by_load(records):
     return recs
 
 def main_ranker(options):
+    from multiprocessing import Process, Manager, Lock
     # LOAD RANKER
     ranker = Ranker()
     if options.seed_presence == "remove": # TODO: Probably, this is not necessary right here but on worker_ranker
@@ -487,7 +472,7 @@ def main_ranker(options):
         if options.threads > 1:
             worker_threads = options.threads - 1
             seeds.sort(reverse=True, key=lambda x: len(x[1]))
-            seeds = sort_records_by_load(seeds)
+            seeds = sort_records_by_load(seeds, chunk_size)
         else:
             worker_threads = options.threads 
         for i in range(worker_threads):
@@ -543,9 +528,15 @@ def main_text2binary_matrix(options):
         x_axis_file=x_axis_file, y_axis_file=y_axis_file, 
         x_idx_file=options.rowids_index, y_idx_file=options.colids_index,
         format_type=options.input_type, symm=options.symmetric,
-        init_matrix_type = options.init_matrix_type, output_matrix_type=options.output_matrix_type)
-
-    # bsr, coo, csc, csr, dia, dok, lil
+        init_matrix_format = options.loading_matrix_format, output_matrix_format=options.output_matrix_format)
+    
+    if options.filter_by_nodes:
+        nodes_to_filter = []
+        with open(options.filter_by_nodes, "r") as f:
+            for line in f:
+                node = line.strip()
+                nodes_to_filter.append(node)
+        matrix, rowIds, colIds = pxc.filter_matrix_by_nodes(matrix, rowIds, colIds, nodes_to_filter)
 
     if options.umap:
         matrix = pxc.data2umap(matrix, n_neighbors = 30, min_dist = 0.1, n_components = 2, 
@@ -578,10 +569,20 @@ def main_text2binary_matrix(options):
             for row in stats:
                 f.write("\t".join([str(item) for item in row]) + "\n")
 
-    pxc.save(matrix, options.output_file, 
-        x_axis_names=rowIds, x_axis_file=options.output_file+"_rowIds.lst", 
-        y_axis_names=colIds, y_axis_file=options.output_file+"_colIds.lst", 
-        format_type=options.output_type, symm = options.symmetric, output_matrix_type=options.output_matrix_type)
+    if options.output_type != "pair":
+        pxc.save(matrix, options.output_file, 
+            x_axis_names=rowIds, x_axis_file=options.output_file+"_rowIds.lst", 
+            y_axis_names=colIds, y_axis_file=options.output_file+"_colIds.lst", 
+            format_type=options.output_type, symm = options.symmetric, 
+            input_matrix_type=options.output_matrix_format,
+            output_matrix_format=options.write_matrix_format)
+    else:
+        pxc.save(matrix, options.output_file, 
+            x_axis_names=rowIds, x_axis_file=options.output_file+"_rowIds.lst", 
+            y_axis_names=colIds, y_axis_file=options.output_file+"_colIds.lst", 
+            format_type=options.output_type, symm = options.symmetric, 
+            input_matrix_type=options.output_matrix_format,
+            output_matrix_format="dense")
 
 # METHODS FOR NETANALYZER
 #########################

{netanalyzer-1.1.0 → netanalyzer-1.1.2}/src/NetAnalyzer/net_plotter.py

@@ -1,16 +1,9 @@
-import os
-import re
-import sys
-import graphviz
-import json
-import base64
+import os, re, graphviz, json, pickle, random
 import igraph as ig
 from igraph.layout import Layout
 import matplotlib as mpl
-import random
 import numpy as np
-import pickle
-from py_report_html import Py_report_html
+from py_report_html.py_report_html import Py_report_html
 import networkx as nx
 
 class Net_plotter:

{netanalyzer-1.1.0 → netanalyzer-1.1.2}/src/NetAnalyzer/netanalyzer.py

@@ -1,26 +1,17 @@
-import random
-import sys 
-import re
-import copy
+import random, sys , re, copy, math, itertools, warnings, logging
 import networkx as nx
-import math
 import numpy as np
-import scipy.stats as stats
 import pandas as pd
-import statsmodels.api as sm
-import itertools
-import warnings
-import logging
-from cdlib import algorithms, viz, evaluation
-from cdlib import NodeClustering
-from NetAnalyzer.adv_mat_calc import Adv_mat_calc
+import scipy.stats as stats
+from scipy.stats import zscore
+from cdlib import evaluation, NodeClustering
+
 import py_exp_calc.exp_calc as pxc
+from py_cmdtabs.cmdtabs import CmdTabs
+
+from NetAnalyzer.adv_mat_calc import Adv_mat_calc
 from NetAnalyzer.net_plotter import Net_plotter
 #from NetAnalyzer.graph2sim import Graph2sim
-from sklearn.preprocessing import StandardScaler
-from sklearn.decomposition import PCA
-from scipy.stats import zscore
-from py_cmdtabs.cmdtabs import CmdTabs
 # https://stackoverflow.com/questions/60392940/multi-layer-graph-in-networkx
 # http://mkivela.com/pymnet
 
@@ -180,7 +171,7 @@ class NetAnalyzer:
 
     def link_ontology(self, ontology_file_path, layer_name):
         import py_semtools # For external_data
-        from py_semtools import Ontology
+        from py_semtools.ontology import Ontology
         if ontology_file_path not in self.loaded_obos: #Load new ontology
             ontology = Ontology(file = ontology_file_path, load_file = True)
             ontology.precompute()
@@ -388,6 +379,7 @@ class NetAnalyzer:
                             fmt='edgelist',
                             validation_method=pvalue_adj_method)
         relations = [[rowIds[relation[0]], rowIds[relation[1]], 1] for relation in relations] # TODO: Check 0-based numeration.
+        self.association_values['bicm'] = relations
         return relations
 
 
@@ -421,6 +413,8 @@ class NetAnalyzer:
         return relations
 
     def get_pca_associations(self, layers, base_layer, n_components = 2, coords2sim_type = "dotProduct"):
+        from sklearn.preprocessing import StandardScaler
+        from sklearn.decomposition import PCA
         # TODO: Try to select the correct number of n_componentes (automatically)
         biadj_matrix = pxc.dig(self.matrices,"adjacency_matrices",tuple(layers),base_layer)
         if biadj_matrix is None:
@@ -573,6 +567,7 @@ class NetAnalyzer:
         return relations
 
     def adjust_pval_association(self, associations, method): # TODO TEST
+        import statsmodels.api as sm
         pvals = np.array([val[2] for val in associations])
         adj_pvals =  sm.stats.multipletests(pvals, method=method, is_sorted=False, returnsorted=False)[1] #2expcalc?
         for idx, adj_pval in enumerate(adj_pvals):
@@ -764,7 +759,7 @@ class NetAnalyzer:
 
     def get_similarity(self, layers, base_layer, sim_type='lin', options={}, output_filename=None, outFormat='pair', add_to_object= False):
         import py_semtools # For external_data
-        from py_semtools import Ontology
+        from py_semtools.ontology import Ontology
         # options--> options['term_filter'] = GO:00001
         ontology = self.layer_ontologies[base_layer]
         relations = self.get_layers_as_dict(layers, base_layer)
@@ -1006,6 +1001,7 @@ class NetAnalyzer:
         return comm_nodes
 
     def get_clusters_by_algorithm(self, cluster_method, clust_kwargs={}):
+        from cdlib import algorithms
         if(cluster_method == 'leiden'):
             communities = algorithms.leiden(self.graph, weights='weight', **clust_kwargs)
         elif(cluster_method == 'louvain'):

{netanalyzer-1.1.0 → netanalyzer-1.1.2}/src/NetAnalyzer/ranker.py

@@ -1,6 +1,5 @@
 import numpy as np
 import os, re
-from itertools import combinations
 from sklearn.model_selection import KFold, LeaveOneOut
 from NetAnalyzer.adv_mat_calc import Adv_mat_calc
 from NetAnalyzer.seed_parser import SeedParser
@@ -9,7 +8,6 @@ import py_exp_calc.exp_calc as pxc
 import networkx as nx
 import random 
 from sklearn.linear_model import LogisticRegression
-from sklearn.model_selection import train_test_split
 
 class Ranker:
 

{netanalyzer-1.1.0 → netanalyzer-1.1.2}/src/NetAnalyzer/templates/net_explorer.txt

@@ -26,8 +26,9 @@
     
     node2seed = {}
     for seed, nodes in plotter.hash_vars["seeds2explore"].items():
-        for node in nodes:
-            if not node2seed.get(node): node2seed[node] = seed
+        if nodes:
+            for node in nodes:
+                if not node2seed.get(node): node2seed[node] = seed
 
     node2group = {}
     if plotter.hash_vars["groups2explore"]:

{netanalyzer-1.1.0 → netanalyzer-1.1.2}/src/NetAnalyzer.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: NetAnalyzer
-Version: 1.1.0
+Version: 1.1.2
 Summary: Python package for network analysis, operations and priorization.
 Home-page: https://github.com/seoanezonjic/NetAnalyzer/
 Author: seoanezonjic
@@ -15,7 +15,7 @@ License-File: LICENSE.txt
 Requires-Dist: importlib-metadata; python_version < "3.8"
 Requires-Dist: NetworkX
 Requires-Dist: numpy
-Requires-Dist: scipy==1.13.1
+Requires-Dist: scipy
 Requires-Dist: statsmodels
 Requires-Dist: graphviz
 Requires-Dist: mako
@@ -25,7 +25,7 @@ Requires-Dist: scikit-learn
 Requires-Dist: py_semtools
 Requires-Dist: umap-learn
 Requires-Dist: py_report_html
-Requires-Dist: gensim==4.3.3
+Requires-Dist: gensim
 Requires-Dist: pecanpy
 Requires-Dist: typing_extensions
 Requires-Dist: py_cmdtabs
@@ -33,6 +33,7 @@ Requires-Dist: py_exp_calc
 Requires-Dist: clusim
 Requires-Dist: nodevectors
 Requires-Dist: torch
+Requires-Dist: bicm
 Provides-Extra: testing
 Requires-Dist: setuptools; extra == "testing"
 Requires-Dist: pytest; extra == "testing"
@@ -88,3 +89,5 @@ This package is designed to perform various steps in network analysis and proces
 * Net plotting: Provides several tools for graphing networks from different net plotter packages (igraph, cytoscape, graphviz).
 
 Please, cite this library as: Rojano E., Seoane-Zonjic P., Bueno-Amorós A., Perkins JR., and Ranea JAG. Revealing the Relationship Between Human Genome Regions and Pathological Phenotypes Through Network Analysis. Lecture Notes in Computer Science, DOI: 10.1007/978-3-319-56148-6_17.
+
+See https://github.com/seoanezonjic/NetAnalyzer

{netanalyzer-1.1.0 → netanalyzer-1.1.2}/src/NetAnalyzer.egg-info/SOURCES.txt

@@ -31,7 +31,6 @@ src/NetAnalyzer/main_modules.py
 src/NetAnalyzer/net_parser.py
 src/NetAnalyzer/net_plotter.py
 src/NetAnalyzer/netanalyzer.py
-src/NetAnalyzer/performancer.py
 src/NetAnalyzer/ranker.py
 src/NetAnalyzer/seed_parser.py
 src/NetAnalyzer.egg-info/PKG-INFO
@@ -40,6 +39,8 @@ src/NetAnalyzer.egg-info/dependency_links.txt
 src/NetAnalyzer.egg-info/entry_points.txt
 src/NetAnalyzer.egg-info/not-zip-safe
 src/NetAnalyzer.egg-info/requires.txt
+src/NetAnalyzer.egg-info/scm_file_list.json
+src/NetAnalyzer.egg-info/scm_version.json
 src/NetAnalyzer.egg-info/top_level.txt
 src/NetAnalyzer/templates/net_explorer.txt
 src/NetAnalyzer/templates/network.txt