diff --git a/src/find_interaction_cluster/community_finder.py b/src/find_interaction_cluster/community_finder.py
index a7a36c611262e2fd1929b1f9459d7ac7a260fa53..cec2033276b1b13153fdb4b3addb0e889cd31b3d 100644
--- a/src/find_interaction_cluster/community_finder.py
+++ b/src/find_interaction_cluster/community_finder.py
@@ -24,6 +24,7 @@ import matplotlib.cm as cm
from matplotlib.colors import to_rgba
from itertools import product
import multiprocessing as mp
+import json
def get_nodes(interaction: np.array) -> np.array:
@@ -67,6 +68,24 @@ def lighten_color(color: np.array, lighten: float = 1):
return color
+def write_cytoscape_graph(graph: nx.Graph, dic_community: Dict[str, str],
+ outfile: str):
+ """
+ Write a dictionary in cyjs format usable by cytoscape.
+
+ :param graph: The network
+ :param dic_community: dictionary linking each njode to it's community.
+ :param outfile: The name of the graph
+ """
+ data = nx.cytoscape_data(graph)
+ for d in data['elements']['nodes']:
+ exon = d['data']['id']
+ d['data']['community'] = dic_community[exon]['num']
+ res = json.dumps(data)
+ with open(outfile, 'w') as f:
+ f.write(res)
+
+
def find_communities(graph: nx.Graph, project: str
) -> Tuple[pd.DataFrame, Dict]:
"""
@@ -78,14 +97,15 @@ def find_communities(graph: nx.Graph, project: str
to wich each exon belong
"""
logging.debug("Finding community ...")
- communities_generator = community.label_propagation_communities(graph)
+ communities_generator = community.asyn_lpa_communities(graph)
communities = list(communities_generator)
dic_community = {}
cov = round(community.coverage(graph, communities), 2)
- perf = np.nan # community.performance(graph, communities)
+ #Â perf = community.performance(graph, communities)
+ modularity = community.modularity(graph, communities, weight='X')
d = {'community': [], 'nodes': [], 'edges' : [], 'EC': [], 'HCS': [],
'%E vs E in complete G': [],
- 'cov': [], 'perf': [], 'exons': []}
+ 'cov': [], 'modularity': [], 'exons': []}
colors = cm.hsv(np.linspace(0, 1, len(communities)))
for k, c in enumerate(communities):
subg = nx.subgraph(graph, c)
@@ -106,9 +126,11 @@ def find_communities(graph: nx.Graph, project: str
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['exons'].append(', '.join(sorted(list(c))))
d['cov'].append(cov)
- d['perf'].append(perf)
+ d['modularity'].append(round(modularity, 5))
+ if nb_nodes <= 9:
+ graph.remove_nodes_from(c)
d['project'] = [project] * len(d['community'])
df = pd.DataFrame(d)
return df, dic_community
@@ -121,7 +143,7 @@ def create_figure(graph: nx.Graph, outfile: Path, dic_community: Dict,
:param graph: The network object
:param outfile: File were the figure will be created
- :param dic_community: dictionary linking each njode to it's community.
+ :param dic_community: dictionary linking each node to it's community.
:param title: The title of the figure
"""
logging.debug("Creating figure")
@@ -130,7 +152,7 @@ def create_figure(graph: nx.Graph, outfile: Path, dic_community: Dict,
middle_x = []
middle_y = []
weight = []
- nodes = nx.spring_layout(graph, seed=1)
+ nodes = nx.nx_pydot.graphviz_layout(graph, prog="neato")
for edge in graph.edges():
x0, y0 = nodes[edge[0]]
x1, y1 = nodes[edge[1]]
@@ -227,7 +249,8 @@ def get_figure_title(project, weight, global_weight, same_gene):
def community_finder(weight: int, global_weight: int, project: str = "",
- same_gene=True, logging_level: str = "DISABLE"):
+ same_gene=True, html_fig: bool = False,
+ logging_level: str = "DISABLE"):
"""
Find communities inside co-localisation between exons found in \
a ChIA-PET project.
@@ -241,6 +264,7 @@ def community_finder(weight: int, global_weight: int, project: str = "",
:param same_gene: Say if we consider as co-localised, exons within the \
same gene (True) or not (False) (default False)
:param logging_level: The level of data to display (default 'DISABLE')
+ :param html_fig: True to create an html figure, false else
"""
ConfigGraph.output_folder.mkdir(exist_ok=True, parents=True)
logging_def(ConfigGraph.output_folder, __file__, logging_level)
@@ -249,13 +273,14 @@ def community_finder(weight: int, global_weight: int, project: str = "",
global_weight, same_gene, True)
graph = create_graph(interaction)
df, dic_community = find_communities(graph, project)
- outfile = ConfigGraph.get_community_file(project, weight, global_weight,
- same_gene, is_fig=False)
- df.to_csv(outfile, sep="\t", index=False)
- figure = ConfigGraph.get_community_file(project, weight, global_weight,
- same_gene, is_fig=True)
- fig_title = get_figure_title(project, weight, global_weight, same_gene)
- create_figure(graph, figure, dic_community, fig_title)
+ outfiles = [ConfigGraph.get_community_file(
+ project, weight, global_weight, same_gene, ext)
+ for ext in ['.txt', '.cyjs', '.html']]
+ df.to_csv(outfiles[0], sep="\t", index=False)
+ write_cytoscape_graph(graph, dic_community, outfiles[1])
+ if html_fig:
+ fig_title = get_figure_title(project, weight, global_weight, same_gene)
+ create_figure(graph, outfiles[2], dic_community, fig_title)
def get_projects(global_weight: int) -> List[str]:
@@ -306,7 +331,7 @@ def get_projects_name(global_weights: List[int]) -> Tuple[List[str], Dict]:
def multiple_community_launcher(ps: int, weights: List[int],
global_weights: List[int],
- same_gene: bool,
+ same_gene: bool, html_fig: bool = False,
logging_level: str = "DISABLE"):
"""
:param ps: The number of processes we want to use.
@@ -317,6 +342,7 @@ def multiple_community_launcher(ps: int, weights: List[int],
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 html_fig: True to create an html figure, false else
:param logging_level: Level of information to display
"""
ConfigGraph.community_folder.mkdir(exist_ok=True, parents=True)
@@ -331,7 +357,7 @@ def multiple_community_launcher(ps: int, weights: List[int],
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]
+ args = [weight, global_weight, project, same_gene, html_fig]
processes.append(pool.apply_async(community_finder, args))
for proc in processes:
proc.get(timeout=None)