src/find_interaction_cluster/graph_figures/__main__.py: add a parameter iteration and community

src/find_interaction_cluster/graph_figures/__main__.py

@@ -12,11 +12,14 @@ from .graph_functions import create_graph_figure, create_many_graph_figures
 
 @lp.parse(weight=range(1, 11), global_weight=range(11),
           feature=('gene', 'exon'), reg=("reg", "down", "up"))
-def launcher(sf_name: str, reg: str, weight: int,
+def launcher(ps: int, sf_name: str, reg: str, weight: int,
              global_weight: int, inflation: float, same_gene: bool = True,
              cell_line: str = "ALL", project: str = 'GSM1018963_GSM1018964',
-             feature: str = "gene", threshold: float = 0.1, min_reg: int = 2):
+             feature: str = "gene", threshold: float = 0.1, min_reg: int = 2,
+             iteration: int = 0, min_community: int = 3):
     """
+    :param ps: The number of processes to create (only used if sf_name \
+    equals ALL).
     :param project: A project name of interest. Used only if \
     global_weight is 0 (default GSM1018963_GSM1018964)
     :param weight: The weight of interaction to consider
@@ -38,16 +41,22 @@ def launcher(sf_name: str, reg: str, weight: int,
     (default 0.1)
     :param min_reg: The minimum of regulated exon in a community to \
     take it into account (default 2)
+    :param iteration: If this parameter is greater or equal to 20 then a \
+    permutation test is made to find the significantly enriched communities. \
+    Below 20, significant communities are found
+    :param min_community: The minimum number of enriched community \
+    required to produce a figure
     """
     if feature == "gene" and not same_gene:
         print("Warning: setting same_gene to True")
     if sf_name != "ALL":
         create_graph_figure(project, weight, global_weight, same_gene,
                             inflation, cell_line, feature, sf_name, reg,
-                            threshold, min_reg)
+                            threshold, min_reg, iteration, min_community)
     else:
-        create_many_graph_figures(project, weight, global_weight, same_gene,
-                                  inflation, cell_line, feature, threshold,
-                                  min_reg)
+        create_many_graph_figures(ps, project, weight, global_weight,
+                                  same_gene, inflation, cell_line,
+                                  feature, threshold, min_reg, iteration,
+                                  min_community)
 
 launcher()
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