From 39d972e6fc816dfda9ab5dcb741079d12fe9f3d7 Mon Sep 17 00:00:00 2001
From: Fontrodona Nicolas <nicolas.fontrodona@ens-lyon.fr>
Date: Fri, 26 Jun 2020 17:27:50 +0200
Subject: [PATCH] src/find_interaction_cluster/community_finder.py: creation of
lighten_color and modification of find_communities to add some data to the
communities find and to change the color of the communities in function of
those data + creation of multiple_community_launcher to find communities for
many projects or wieghts
---
.../community_finder.py | 149 ++++++++++++++----
1 file changed, 121 insertions(+), 28 deletions(-)
diff --git a/src/find_interaction_cluster/community_finder.py b/src/find_interaction_cluster/community_finder.py
index 8974a385..a7a36c61 100644
--- a/src/find_interaction_cluster/community_finder.py
+++ b/src/find_interaction_cluster/community_finder.py
@@ -19,13 +19,11 @@ import logging
import plotly.graph_objects as go
import plotly
from pathlib import Path
-from typing import Tuple, Dict
+from typing import Tuple, Dict, List
import matplotlib.cm as cm
-from matplotlib.colors import rgb2hex
-
-
-class BadProjectName(Exception):
- pass
+from matplotlib.colors import to_rgba
+from itertools import product
+import multiprocessing as mp
def get_nodes(interaction: np.array) -> np.array:
@@ -56,6 +54,19 @@ def create_graph(interaction: np.array) -> nx.Graph:
return graph
+def lighten_color(color: np.array, lighten: float = 1):
+ """
+
+ :param color: A tuple of 3 float
+ :param lighten: The value to add to color.
+ :return: The color lightened
+ """
+ color = list(to_rgba(color))
+ color = [int(c * 255) for c in color[0:3]] + [lighten]
+ color = 'rgba(' + ', '.join(map(str, color)) + ')'
+ return color
+
+
def find_communities(graph: nx.Graph, project: str
) -> Tuple[pd.DataFrame, Dict]:
"""
@@ -67,24 +78,37 @@ def find_communities(graph: nx.Graph, project: str
to wich each exon belong
"""
logging.debug("Finding community ...")
- communities_generator = community.girvan_newman(graph)
- communities = next(communities_generator)
+ communities_generator = community.label_propagation_communities(graph)
+ communities = list(communities_generator)
dic_community = {}
- cov = community.coverage(graph, communities)
- perf = community.performance(graph, communities)
- d = {'community': [], 'size': [], 'cov': [], 'perf': [], 'exons': []}
- colors = cm.rainbow(np.linspace(0, 1, len(communities)))
+ cov = round(community.coverage(graph, communities), 2)
+ perf = np.nan # community.performance(graph, communities)
+ d = {'community': [], 'nodes': [], 'edges' : [], 'EC': [], 'HCS': [],
+ '%E vs E in complete G': [],
+ 'cov': [], 'perf': [], 'exons': []}
+ colors = cm.hsv(np.linspace(0, 1, len(communities)))
for k, c in enumerate(communities):
- clen = len(c)
+ subg = nx.subgraph(graph, c)
+ nb_nodes = len(c)
+ nb_edges = len(subg.edges)
+ edge_connectivity = nx.edge_connectivity(subg)
+ is_hc = 'yes' if edge_connectivity > nb_nodes / 2 else 'no'
for exon in c:
dic_community[exon] = {'num': f'C{k + 1}',
- 'col': rgb2hex(colors[k][:3])
- if clen > 2 else 'white'}
+ 'col': lighten_color(colors[k])
+ if is_hc == 'yes' else
+ (lighten_color(colors[k], 0.1) if nb_nodes > 2 else 'white')
+ }
d['community'].append(f'C{k + 1}')
- d['size'].append(len(list(c)))
+ d['nodes'].append(nb_nodes)
+ d['edges'].append(nb_edges)
+ d['EC'].append(edge_connectivity)
+ d['HCS'].append(is_hc)
+ d['%E vs E in complete G'].append(round(
+ nb_edges / (nb_nodes * (nb_nodes - 1) / 2) * 100, 2))
d['exons'].append(', '.join(list(c)))
- d['cov'].append(round(cov, 5))
- d['perf'].append(round(perf, 5))
+ d['cov'].append(cov)
+ d['perf'].append(perf)
d['project'] = [project] * len(d['community'])
df = pd.DataFrame(d)
return df, dic_community
@@ -220,16 +244,6 @@ def community_finder(weight: int, global_weight: int, project: str = "",
"""
ConfigGraph.output_folder.mkdir(exist_ok=True, parents=True)
logging_def(ConfigGraph.output_folder, __file__, logging_level)
- if project != "" and global_weight != 0:
- msg = "A project name was given given along with a " \
- "global weight != 0 ! You should not give a project name if " \
- "you want to concider many project together"
- logging.exception(msg)
- raise BadProjectName(msg)
- if project == "" and global_weight == 0:
- msg = "A project name must be given when global weight == 0"
- logging.exception(msg)
- raise BadProjectName
cnx = sqlite3.connect(ConfigGraph.db_file)
interaction = get_project_colocalisation(cnx, project, weight,
global_weight, same_gene, True)
@@ -242,3 +256,82 @@ def community_finder(weight: int, global_weight: int, project: str = "",
same_gene, is_fig=True)
fig_title = get_figure_title(project, weight, global_weight, same_gene)
create_figure(graph, figure, dic_community, fig_title)
+
+
+def get_projects(global_weight: int) -> List[str]:
+ """
+ Get projects name.
+
+ :param global_weight: The global weight to consider. if \
+ the global weight is equal to 0 then then density figure are calculated \
+ by project, else all projet are merge together and the interaction \
+ seen in `global_weight` project are taken into account
+ :return: The list of the project to consider
+ """
+ if global_weight != 0:
+ return [f'Global-weight-{global_weight}']
+ else:
+ cnx = sqlite3.connect(ConfigGraph.db_file)
+ c = cnx.cursor()
+ query = f"SELECT DISTINCT id_sample " \
+ f"FROM cin_projects " \
+ f"WHERE id_sample = 'GSM1872888' "
+ c.execute(query)
+ res = list(np.asarray(c.fetchall()).flatten())
+ c.close()
+ cnx.close()
+ return res
+
+def get_projects_name(global_weights: List[int]) -> Tuple[List[str], Dict]:
+ """
+ Get projects name given a list of global_weight and a dictionary linking,
+ each project name to it's corresponding global weight.
+
+ :param global_weight: The list of global weights to consider. if \
+ the global weight is equal to 0 then then density figure are calculated \
+ by project, else all projet are merge together and the interaction \
+ seen in `global_weight` project are taken into account
+ :return: project names and a dictionary linking,
+ each name to it's corresponding global weight.
+ """
+ dic = {}
+ projects = []
+ for global_weight in global_weights:
+ tmp = get_projects(global_weight)
+ projects += tmp
+ for p in tmp:
+ dic[p] = global_weight
+ return projects, dic
+
+
+def multiple_community_launcher(ps: int, weights: List[int],
+ global_weights: List[int],
+ same_gene: bool,
+ logging_level: str = "DISABLE"):
+ """
+ :param ps: The number of processes we want to use.
+ :param weights: The list of weights of interaction to consider
+ :param global_weights: The list global weights to consider. if \
+ the global weight is equal to 0 then then density figure are calculated \
+ by project, else all projcet are merge together and the interaction \
+ seen in `global_weight` project are taken into account
+ :param same_gene: Say if we consider as co-localised exon within the \
+ same gene
+ :param logging_level: Level of information to display
+ """
+ ConfigGraph.community_folder.mkdir(exist_ok=True, parents=True)
+ logging_def(ConfigGraph.community_folder, __file__, logging_level)
+ global_weights = list(np.unique(global_weights))
+ weights = list(np.unique(weights))
+ projects, dic_project = get_projects_name(global_weights)
+ condition = list(product(projects, weights))
+ processes = []
+ pool = mp.Pool(processes=min(ps, len(condition)))
+ for project, weight in condition:
+ global_weight = dic_project[project]
+ logging.info(f'Finding community for project : {project}, '
+ f'global_weight : {global_weight}, weight: {weight}')
+ args = [weight, global_weight, project, same_gene]
+ processes.append(pool.apply_async(community_finder, args))
+ for proc in processes:
+ proc.get(timeout=None)
--
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