diff --git a/Analyse.hs b/Analyse.hs
--- a/Analyse.hs
+++ b/Analyse.hs
@@ -43,7 +43,7 @@
 --   'HaskellModules' form.
 analyse            :: (RandomGen g) => g -> [ModName] -> ParsedModules
                    -> [DocElement]
-analyse g exps hms = [ analyseModules hms
+analyse g exps hms = [ analyseEverything g exps hms
                      , analyseImports exps hms
-                     , analyseEverything g exps hms
+                     , analyseModules hms
                      ]
diff --git a/Analyse/Utils.hs b/Analyse/Utils.hs
--- a/Analyse/Utils.hs
+++ b/Analyse/Utils.hs
@@ -128,7 +128,7 @@
                                           nAttr
                                           callAttributes'
     where
-      gAttrs = [NodeAttrs [Margin . PVal $ PointD 0.2 0.2]] -- [GraphAttrs [Label $ StrLabel t]]
+      gAttrs = [NodeAttrs [Margin . PVal $ PointD 0.5 0.2]] -- [GraphAttrs [Label $ StrLabel t]]
       dg' = updateGraph compactSame dg
       -- Possible clustering problem
       toClust = clusterEntity -- bool clusterEntity clusterEntityM' $ isJust mm
@@ -146,7 +146,7 @@
                                        nAttr
                                        callAttributes'
     where
-      gAttrs = [] -- [GraphAttrs [Label $ StrLabel t]]
+      gAttrs = [NodeAttrs [Margin . PVal $ PointD 0.5 0.2]] -- [GraphAttrs [Label $ StrLabel t]]
       dg' = updateGraph (compactSame . collapseStructures') dg
       rs = getRoots dg
       ls = getLeaves dg
@@ -217,24 +217,24 @@
 callAttributes' (_,_,(n,ct)) = PenWidth (fromIntegral n)
                                : callAttributes ct
 
-clustAttributes               :: EntClustType -> Attributes
-clustAttributes (ClassDefn c) = [ Label . StrLabel $ "Class: " ++ c
-                                , Style [SItem Filled [], SItem Rounded []]
-                                , FillColor $ ColorName "rosybrown1"
-                                ]
-clustAttributes (DataDefn d)  = [ Label . StrLabel $ "Data: " ++ d
-                                , Style [SItem Filled [], SItem Rounded []]
-                                , FillColor $ ColorName "papayawhip"
-                                ]
-clustAttributes (ClassInst d) = [ Label . StrLabel $ "Instance for: " ++ d
-                                , Style [SItem Filled [], SItem Rounded []]
-                                , FillColor $ ColorName "slategray1"
-                                ]
-clustAttributes DefInst       = [ Label . StrLabel $ "Default Instance"
+clustAttributes                 :: EntClustType -> Attributes
+clustAttributes (ClassDefn c)   = [ Label . StrLabel $ "Class: " ++ c
+                                  , Style [SItem Filled [], SItem Rounded []]
+                                  , FillColor $ ColorName "rosybrown1"
+                                  ]
+clustAttributes (DataDefn d)    = [ Label . StrLabel $ "Data: " ++ d
+                                  , Style [SItem Filled [], SItem Rounded []]
+                                  , FillColor $ ColorName "papayawhip"
+                                  ]
+clustAttributes (ClassInst _ d) = [ Label . StrLabel $ "Instance for: " ++ d
                                 , Style [SItem Filled [], SItem Rounded []]
                                 , FillColor $ ColorName "slategray1"
                                 ]
-clustAttributes (ModPath p)   = [ Label $ StrLabel p ]
+clustAttributes DefInst{}       = [ Label . StrLabel $ "Default Instance"
+                                  , Style [SItem Filled [], SItem Rounded []]
+                                  , FillColor $ ColorName "slategray1"
+                                  ]
+clustAttributes (ModPath p)     = [ Label $ StrLabel p ]
 
 clustAttributes' :: EntClustType -> [GlobalAttributes]
 clustAttributes' = return . GraphAttrs . clustAttributes
@@ -257,7 +257,7 @@
                                             nAttr
                                             callAttributes'
     where
-      gAttrs = [] -- [GraphAttrs [Label $ StrLabel t]]
+      gAttrs = [NodeAttrs [Margin . PVal $ PointD 0.5 0.2]] -- [GraphAttrs [Label $ StrLabel t]]
       cAttr = [GraphAttrs [ Style [SItem Filled []]
                           , FillColor $ ColorName "wheat1"
                           ]
@@ -280,23 +280,24 @@
                                          nAttr
                                          (const [])
     where
-      cID s = bool (Just $ Str s) Nothing $ null s
-      gAttrs = [] --[GraphAttrs [Label $ StrLabel t]]
+      cID s = bool (Just $ Str s) Nothing $ (not . null) s
+      gAttrs = [NodeAttrs [Margin . PVal $ PointD 0.5 0.2]] --[GraphAttrs [Label $ StrLabel t]]
       cAttr p = [GraphAttrs [Label $ StrLabel p]]
       rs = I.fromList $ applyAlg rootsOf' dg
       ls = I.fromList $ applyAlg leavesOf' dg
       es = I.fromList $ wantedRootNodes dg
       nAttr (n,m) = [ Label $ StrLabel m
-                    , Color [ColorName $ mCol rs ls es n]
+                    , FillColor $ ColorName $ mCol rs ls es n
+                    , Style [SItem Filled []]
                     , Shape Tab
                     ]
 
 mCol :: IntSet -> IntSet -> IntSet -> Node -> String
 mCol rs ls es n
-    | isR && not isE = "red"
-    | isR            = "mediumblue"
-    | isL            = "forestgreen"
-    | otherwise      = "black"
+    | isR && not isE = "crimson"
+    | isR            = "gold"
+    | isL            = "cyan"
+    | otherwise      = "bisque"
     where
       isR = n `I.member` rs
       isL = n `I.member` ls
diff --git a/ChangeLog b/ChangeLog
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,3 +1,15 @@
+Changes since 0.5.2.0
+=====================
+
+* Shift overall analysis to the top and per-module analysis to the
+  end, as suggested by Duncan Coutts.
+
+* Graph drawing fixups: instances are now drawn correctly, and the
+  module graph now has modules located in the correct directory.
+
+* Improve some graph drawing aspects (node margins, colours for module
+  graphs, etc.).
+
 Changes since 0.5.1.0
 =====================
 
diff --git a/Main.hs b/Main.hs
--- a/Main.hs
+++ b/Main.hs
@@ -271,6 +271,6 @@
                       , Emphasis $ Text programmeName
                       , Text " is "
                       , Bold $ Text "not"
-                      , Text " a refactoring tool, and does not take into \
-                             \account Class declarations and record functions."
+                      , Text " a refactoring tool, and it's usage of Classes is\
+                              \ not yet perfect."
                       ]
diff --git a/Parsing/Types.hs b/Parsing/Types.hs
--- a/Parsing/Types.hs
+++ b/Parsing/Types.hs
@@ -302,23 +302,23 @@
                    (Constructor d)     -> C $ DataDefn d
                    (RecordFunction d)  -> C $ DataDefn d
                    (ClassFunction c)   -> C $ ClassDefn c
-                   (DefaultInstance c) -> C (ClassDefn c) . C DefInst
-                   (ClassInstance c d) -> C (ClassDefn c) . C (ClassInst d)
+                   (DefaultInstance c) -> C (ClassDefn c) . C (DefInst c)
+                   (ClassInstance c d) -> C (ClassDefn c) . C (ClassInst c d)
                    _                   -> id
 
 data EntClustType = ClassDefn ClassName
                   | DataDefn DataType
-                  | ClassInst DataType
-                  | DefInst
+                  | ClassInst ClassName DataType
+                  | DefInst ClassName
                   | ModPath String
                     deriving (Eq, Ord, Show, Read)
 
-ctypeID               :: EntClustType -> Maybe GraphID
-ctypeID (ClassDefn c) = Just . Str $ "Class_" ++ escID c
-ctypeID (DataDefn d)  = Just . Str $ "Data_" ++ escID d
-ctypeID (ClassInst d) = Just . Str $ "Inst_For_" ++ escID d
-ctypeID DefInst       = Just . Str $ "DefaultInstance"
-ctypeID (ModPath p)   = Just . Str $ "Directory_" ++ escID p
+ctypeID                 :: EntClustType -> Maybe GraphID
+ctypeID (ClassDefn c)   = Just . Str $ "Class_" ++ escID c
+ctypeID (DataDefn d)    = Just . Str $ "Data_" ++ escID d
+ctypeID (ClassInst c d) = Just . Str $ "Class_" ++ escID c ++ "_Data_" ++ escID d
+ctypeID (DefInst c)     = Just . Str $ "DefaultInstance_" ++ escID c
+ctypeID (ModPath p)     = Just . Str $ "Directory_" ++ escID p
 
 escID :: String -> String
 escID = filter (\c -> isLetter c || isDigit c || c == '_')
diff --git a/SourceGraph.cabal b/SourceGraph.cabal
--- a/SourceGraph.cabal
+++ b/SourceGraph.cabal
@@ -1,5 +1,5 @@
 Name:                SourceGraph
-Version:             0.5.1.0
+Version:             0.5.2.0
 Synopsis:            Use graph-theory to analyse your code
 Description: {
 Statically analyse Haskell source code using graph-theoretic
diff --git a/TODO b/TODO
--- a/TODO
+++ b/TODO
@@ -12,3 +12,8 @@
 
 * Write a README
 
+* Find where spurious class function entities are coming from.
+
+* Fix up printing of entities for node lists.
+
+* Add a legend.