changes for final sub

examples/matlab/kitchen_sink.m

@@ -32,7 +32,7 @@
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 % Network 2 of 3: the Zachary Karate Club                                 %
-% Feature: a network w/ node names and additional metadata for 2 nodes    %
+% Feature: a network w/ node names and additional (binary ) metadata      %
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
 % Directly specify an edge list.
@@ -87,7 +87,7 @@
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 % Display parameters choices and defaults                                   %
-% Demonstrates: how to fix default behavior for webweb on opening the html  %
+% Demonstrates: how to set default behavior for webweb on opening the html  %
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
 ww.display.networkName = 'tree';
@@ -102,4 +102,4 @@
 ww.display.scaleLinkWidth = 1;
 
 % call webweb
-webweb(ww);
+webweb(ww);

examples/python/kitchen_sink.py

@@ -1,54 +1,78 @@
 from webweb import Web
 import random
 
+# Give the webweb a title.
 web = Web(title='kitchen_sink')
 
 ################################################################################
-# Stochastic Block Model network
+# Network 1 of 3: a stochastic block model (SBM)
+# Features: a network w/ metadata
 ################################################################################
-# let's generate a graph using the Stochastic Block Model
 
-# choose sizes of communities
-c1, c2, c3 = 15, 20, 25
+# Create an empty edge list, to be populated during network construction
+edge_list = []
+
+# group sizes
+group_sizes = [15, 20, 25]
 
-# group memberships, z
-z = [0 for _ in range(c1)] + [1 for _ in range(c2)] + [2 for _ in range(c3)]
+# probability of edges between groups
+node_group = [0 for _ in range(group_sizes[0])]
+node_group += [1 for _ in range(group_sizes[1])] 
+node_group += [2 for _ in range(group_sizes[2])] 
 
 # group affinity matrix
 M = [[ 0.25, 0.02, 0    ],
      [ 0.02, 0.2,  0.02 ],
      [ 0,    0.02, 0.15 ]]
 
 # SBM
-edge_list = []
-for i in range(c1 + c2 + c3):
+for i in range(sum(group_sizes)):
     for j in range(i):
-        if random.random() < M[z[i]][z[j]]:
+        if random.random() < M[node_group[i]][node_group[j]]:
             edge_list.append([i,j])
 
-web.networks.sbm(adjacency=edge_list, metadata={'community': {'values' : z}})
+# create a network called sbm
+web.networks.sbm(
+    # assign its edgelist
+    adjacency=edge_list,
+    # give it the community metadata
+    metadata={'community': 
+        {
+            'values' : node_group,
+            # tell webweb to display the groups categorically
+            'type' : 'categorical',
+        },
+    }
+)
 
 ################################################################################
-# Zachary Karate Club
+# Network 2 of 3: the Zachary Karate Club
+# Feature: a network w/ node names and additional (binary) metadata
 ################################################################################
+
 web.networks.zkc(
     adjacency=[[2,1],[3,1],[3,2],[4,1],[4,2],[4,3],[5,1],[6,1],[7,1],[7,5],[7,6],[8,1],[8,2],[8,3],[8,4],[9,1],[9,3],[10,3],[11,1],[11,5],[11,6],[12,1],[13,1],[13,4],[14,1],[14,2],[14,3],[14,4],[17,6],[17,7],[18,1],[18,2],[20,1],[20,2],[22,1],[22,2],[26,24],[26,25],[28,3],[28,24],[28,25],[29,3],[30,24],[30,27],[31,2],[31,9],[32,1],[32,25],[32,26],[32,29],[33,3],[33,9],[33,15],[33,16],[33,19],[33,21],[33,23],[33,24],[33,30],[33,31],[33,32],[34,9],[34,10],[34,14],[34,15],[34,16],[34,19],[34,20],[34,21],[34,23],[34,24],[34,27],[34,28],[34,29],[34,30],[34,31],[34,32],[34,33]],
+    # assign some metadata to nodes by their id
     nodes={1 : { 'headHoncho' : True}, 34 : {'headHoncho' : True}},
     metadata={
+        # use the reserved keyword 'name' to give names to nodes for displaying
         'name' : {
             'values' : ["Bernita Blizzard", "Lauran Lenahan", "Kallie Kerr", "Yun Yearsley", "Krystina Kehr", "Marisa Mccullough", "Sandra Soderquist", "Latisha Luczynski", "Gertrudis Guadarrama", "Ramonita Raley", "Tessa Tuff", "Michell Murphey", "Juliana Jenny", "Imogene Ivie", "Ricky Revis", "Tonia Tighe", "Lyle Lamanna", "Michael Motto", "Charlie Cartwright", "Aimee Aschenbrenner", "Vi Vallery", "Shaquana Stocking", "Penelope Percival", "Bari Barrentine", "Janie Jeske", "Breann Brodie", "Carmel Clara", "Nada Nicol", "Francisca Fu", "Shyla Schranz", "Clarissa Crooks", "Hilario Holzwarth", "Huong Hodge", "Lavonne Leng",]
         }
     }
 )
+
 ################################################################################
-# Tree/Ring network (N-Cayley tree)
+# Network 3 of 3: Tree/Ring network (N-Cayley tree)
+# Features: a multilayer network with different metadata for each layer
 ################################################################################
-# let's make a tree network with 4 layers and a branching factor of 5
+
 tree_layers = 4
 branching_factor = 5
 
 nodes_queue = [0]
 
+# Create an empty edge list, to be populated during layer construction
 edge_list = []
 nodes = {}
 for tree_layer in range(tree_layers):
@@ -57,7 +81,8 @@
     while len(nodes_queue):
         node = nodes_queue.pop(0)
         nodes[node] = { 'ring' : tree_layer }
-        for _ in range(branching_factor):
+        branches = branching_factor if tree_layer == 0 else branching_factor - 1
+        for _ in range(branches):
             new_node = max(nodes.keys()) + 1
             edge_list.append([node, new_node])
             new_nodes_queue.append(new_node)
@@ -66,12 +91,18 @@
     nodes_queue = new_nodes_queue
     web.networks.tree.add_layer(adjacency=edge_list, nodes=nodes)
 
+# tell webweb to display the metdata categorically
 web.display.metadata = {
     'ring' : {
         'type' : 'categorical',
     }
 }
 
+################################################################################
+# Display parameters choices and defaults
+# Demonstrates: how to set default behavior for webweb on opening the html
+################################################################################
+
 web.display.networkName = 'tree'
 web.display.networkLayer = 3
 web.display.colorBy = 'ring'
@@ -80,7 +111,7 @@
 web.display.charge = 30
 web.display.linkLength = 15
 web.display.colorPalette = 'Greens'
-web.display.scaleLinkOpacity = True
+web.display.scaleLinkOpacity = False
 web.display.scaleLinkWidth = True
 
 # show the visualization