From 68f0af4deb139041fb68782df26e192b8248be38 Mon Sep 17 00:00:00 2001
From: James Hensman <james.hensman@gmail.com>
Date: Wed, 26 Feb 2014 17:13:47 +0000
Subject: [PATCH] fixes in the plotting and in the dot graphing

---
 GPy/core/parameterization/param.py         |  6 +++++-
 GPy/core/parameterization/parameterized.py |  6 +++++-
 GPy/plotting/matplot_dep/base_plots.py     | 20 ++++++++++----------
 GPy/plotting/matplot_dep/models_plots.py   |  2 +-
 4 files changed, 21 insertions(+), 13 deletions(-)

diff --git a/GPy/core/parameterization/param.py b/GPy/core/parameterization/param.py
index b48bec0d..3b08eebd 100644
--- a/GPy/core/parameterization/param.py
+++ b/GPy/core/parameterization/param.py
@@ -65,7 +65,11 @@ class Param(Constrainable, ObservableArray, Gradcheckable):
         node = pydot.Node(id(self), shape='record', label=self.name)
         G.add_node(node)
         for o in self._observer_callables_.keys():
-            print o, self.hirarchy_name()
+            label = o.name if hasattr(o, 'name') else str(o)
+            observed_node = pydot.Node(id(o), label=label)
+            G.add_node(observed_node)
+            edge = pydot.Edge(str(id(self)), str(id(o)), color='darkorange2', arrowhead='vee')
+            G.add_edge(edge)
 
         return node
 
diff --git a/GPy/core/parameterization/parameterized.py b/GPy/core/parameterization/parameterized.py
index 83a62161..fb606278 100644
--- a/GPy/core/parameterization/parameterized.py
+++ b/GPy/core/parameterization/parameterized.py
@@ -77,7 +77,11 @@ class Parameterized(Parameterizable, Pickleable, Gradcheckable):
             G.add_edge(pydot.Edge(node, child_node))
 
         for o in self._observer_callables_.keys():
-            print id(o), self.hirarchy_name()
+            label = o.name if hasattr(o, 'name') else str(o)
+            observed_node = pydot.Node(id(o), label=label)
+            G.add_node(observed_node)
+            edge = pydot.Edge(str(id(self)), str(id(o)), color='darkorange2', arrowhead='vee')
+            G.add_edge(edge)
 
         if iamroot:
             return G
diff --git a/GPy/plotting/matplot_dep/base_plots.py b/GPy/plotting/matplot_dep/base_plots.py
index a9d25223..e86ef6ca 100644
--- a/GPy/plotting/matplot_dep/base_plots.py
+++ b/GPy/plotting/matplot_dep/base_plots.py
@@ -18,17 +18,17 @@ def meanplot(x, mu, color=Tango.colorsHex['darkBlue'], ax=None, fignum=None, lin
     _, axes = ax_default(fignum, ax)
     #here's the mean
     return axes.plot(x,mu,color=color,linewidth=linewidth,**kw)
-    
+
 def gpplot(x,mu,lower,upper,edgecol=Tango.colorsHex['darkBlue'],fillcol=Tango.colorsHex['lightBlue'],ax=None,fignum=None,xlabel='x',ylabel='y',**kwargs):
-    _, axes = ax_default(ax, fignum)
-        
+    _, axes = ax_default(fignum, ax)
+
     mu = mu.flatten()
     x = x.flatten()
     lower = lower.flatten()
     upper = upper.flatten()
 
     plots = []
-    
+
     #here's the mean
     plots.append(meanplot(x, mu, edgecol, axes))
 
@@ -39,15 +39,15 @@ def gpplot(x,mu,lower,upper,edgecol=Tango.colorsHex['darkBlue'],fillcol=Tango.co
     plots.append(axes.fill(np.hstack((x,x[::-1])),np.hstack((upper,lower[::-1])),color=fillcol,**kwargs))
 
     #this is the edge:
-    plots.append(meanplot(x, upper,color=edgecol,linewidth=0.2,axes=axes))
-    plots.append(meanplot(x, lower,color=edgecol,linewidth=0.2,axes=axes))
-    
+    plots.append(meanplot(x, upper,color=edgecol,linewidth=0.2,ax=axes))
+    plots.append(meanplot(x, lower,color=edgecol,linewidth=0.2,ax=axes))
+
     axes.set_xlabel(xlabel)
     axes.set_ylabel(ylabel)
-    
+
     return plots
-    
-    
+
+
 def removeRightTicks(ax=None):
     ax = ax or pb.gca()
     for i, line in enumerate(ax.get_yticklines()):
diff --git a/GPy/plotting/matplot_dep/models_plots.py b/GPy/plotting/matplot_dep/models_plots.py
index 5123f514..d72d2a3e 100644
--- a/GPy/plotting/matplot_dep/models_plots.py
+++ b/GPy/plotting/matplot_dep/models_plots.py
@@ -86,7 +86,7 @@ def plot_fit(model, plot_limits=None, which_data_rows='all',
             m, v, lower, upper = model.predict(Xgrid)
             Y = Y
         for d in which_data_ycols:
-            gpplot(Xnew, m[:, d], lower[:, d], upper[:, d], axes=ax, edgecol=linecol, fillcol=fillcol)
+            gpplot(Xnew, m[:, d], lower[:, d], upper[:, d], ax=ax, edgecol=linecol, fillcol=fillcol)
             ax.plot(X[which_data_rows,free_dims], Y[which_data_rows, d], 'kx', mew=1.5)
 
         #optionally plot some samples