put in grey var that are not input, not output, and not a intermediate var.

theano/printing.py

@@ -361,7 +361,9 @@ def pydotprint(fct, outfile=os.path.join(config.compiledir,'theano.pydotprint.pn
     We print the op of the apply in the Apply box with a number that represent the toposort order of application of those Apply.
     If an Apply have more then 1 input, print add a label to the edge that in the index of the inputs.
 
-    green ellipse are input to the graph and blue ellipse are output of the graph.
+    green ellipse are input to the graph
+    blue ellipse are output of the graph
+    grey ellipse are var generated by the graph that are not output and are not used.
     """
     try:
         import pydot as pd
@@ -428,6 +430,9 @@ def pydotprint(fct, outfile=os.path.join(config.compiledir,'theano.pydotprint.pn
             if out:
                 g.add_edge(pd.Edge(astr,varstr))
                 g.add_node(pd.Node(varstr,color='blue'))
+            elif len(var.clients)==0:
+                g.add_edge(pd.Edge(astr,varstr))
+                g.add_node(pd.Node(varstr,color='grey'))
             elif var.name or not compact:
                 g.add_edge(pd.Edge(astr,varstr))
             else: