added clade_color and clade_shape to cytoscape json

planet/helpers/cytoscape.py

@@ -10,7 +10,8 @@
 from planet.models.relationships.sequence_interpro import SequenceInterproAssociation
 from planet.models.sequences import Sequence
 from planet.models.species import Species
-from utils.color import family_to_shape_and_color
+from planet.models.clades import Clade
+from utils.color import family_to_shape_and_color, index_to_shape_and_color
 
 
 class CytoscapeHelper:
@@ -76,15 +77,24 @@ def add_family_data_nodes(network, family_method_id):
 
         data = {}
 
+        clades = Clade.query.order_by(Clade.species_count).all()
+        clade_list = [c.name for c in clades]
+
         for s in sequence_families:
             data[s.sequence_id] = {}
             data[s.sequence_id]["name"] = s.family.name
             data[s.sequence_id]["id"] = s.gene_family_id
             data[s.sequence_id]["url"] = url_for('family.family_view', family_id=s.gene_family_id)
             if s.family.clade is not None:
+                clade_index = clade_list.index(s.family.clade.name)
+                color, shape = index_to_shape_and_color(clade_index)
+                data[s.sequence_id]["clade_color"] = color
+                data[s.sequence_id]["clade_shape"] = shape
                 data[s.sequence_id]["clade"] = s.family.clade.name
                 data[s.sequence_id]["clade_count"] = s.family.clade.species_count
             else:
+                data[s.sequence_id]["clade_color"] = "#CCC"
+                data[s.sequence_id]["clade_shape"] = "rectangle"
                 data[s.sequence_id]["clade"] = "None"
                 data[s.sequence_id]["clade_count"] = 0
 
@@ -111,13 +121,18 @@ def add_family_data_nodes(network, family_method_id):
                 node["data"]["family_id"] = data[node["data"]["gene_id"]]["id"]
                 node["data"]["family_url"] = data[node["data"]["gene_id"]]["url"]
                 node["data"]["family_clade"] = data[node["data"]["gene_id"]]["clade"]
+                node["data"]["family_clade_color"] = data[node["data"]["gene_id"]]["clade_color"]
+                node["data"]["family_clade_shape"] = data[node["data"]["gene_id"]]["clade_shape"]
                 node["data"]["family_clade_count"] = data[node["data"]["gene_id"]]["clade_count"]
             else:
                 node["data"]["family_name"] = None
                 node["data"]["family_id"] = None
                 node["data"]["family_url"] = None
                 node["data"]["family_color"] = "#CCC"
                 node["data"]["family_shape"] = "rectangle"
+
+                node["data"]["family_clade_color"] = "#CCC"
+                node["data"]["family_clade_shape"] = "rectangle"
                 node["data"]["family_clade"] = "None"
                 node["data"]["family_clade_count"] = 1
 

utils/color.py

@@ -86,6 +86,22 @@ def label_coocurrence(ListOfListOfLabels):
     return lc
 
 
+def index_to_shape_and_color(index):
+    """
+    Returns a tuple (color, shape) from an index
+
+
+    :param index: integer number
+    :return: tuple (color, shape)
+    """
+
+    color_index = index % len(__COLORS)
+    shape_index = index // len(__COLORS)
+    shape_index = shape_index if shape_index < len(__SHAPES) else 0
+
+    return __COLORS[color_index], __SHAPES[shape_index]
+
+
 def family_to_shape_and_color(input_dictionary):
     """
     Takes a dictionary, where key:gene ID, value: ["fam1", "fam2",...]