Packageedu.stanford.covertlab.analysis
Classpublic class HierarchicalClustering

Implements hierarchical agglomerative clustering using the O(n^3) algorithm described in Eisen et al.(1998) and the recursive O(n^4) optimal leaf ordering described in Bar-Joseph et al (2001).

References:


Public Methods
 MethodDefined by
  
averageLinkage(distance:Array, cluster1:Array, cluster2:Array):Number
[static]
HierarchicalClustering
  
cluster(distance:Array, linkage:String, optimizeLeafOrder:Boolean = true, clusters:Array = null, leafOrder:Array = null):Object
[static] hierarchical agglomerative clustering (Eisen et al, 1998).
HierarchicalClustering
  
completeLinkage(distance:Array, cluster1:Array, cluster2:Array):Number
[static]
HierarchicalClustering
  
getLeafOrder(tree:Array):Array
[static]
HierarchicalClustering
  
getLeafPositions(tree:Array):Array
[static]
HierarchicalClustering
  
orderLeafs(v:Array, S:Array):Object
[static] optimal leaf ordering (Bar-Joseph et al, 2001)
HierarchicalClustering
  
pairwiseDistance(vector1:Array, vector2:Array, metric:String, p:Number = 1):Number
[static] pairwise distance
HierarchicalClustering
  
printTree(tree:Array):String
[static]
HierarchicalClustering
  
reverseTree(tree:Array):Array
[static]
HierarchicalClustering
  
singleLinkage(distance:Array, cluster1:Array, cluster2:Array):Number
[static]
HierarchicalClustering
Public Constants
 ConstantDefined by
  DISTANCE_METRIC_CHEBYCHEV : String = "Chebychev"
[static]
HierarchicalClustering
  DISTANCE_METRIC_CITYBLOCK : String = "City Block"
[static]
HierarchicalClustering
  DISTANCE_METRIC_CORRELATION : String = "Correlation"
[static]
HierarchicalClustering
  DISTANCE_METRIC_COSINE : String = "Cosine"
[static]
HierarchicalClustering
  DISTANCE_METRIC_EUCLIDEAN : String = "Euclidean"
[static]
HierarchicalClustering
  DISTANCE_METRIC_HAMMING : String = "Hamming"
[static]
HierarchicalClustering
  DISTANCE_METRIC_JACCARD : String = "Jaccard"
[static]
HierarchicalClustering
  DISTANCE_METRIC_MINKOWSKI : String = "Minkowski"
[static]
HierarchicalClustering
  DISTANCE_METRICS : ArrayCollection
[static]
HierarchicalClustering
  LINKAGE_AVERAGE : String = "Average"
[static]
HierarchicalClustering
  LINKAGE_COMPLETE : String = "Complete"
[static]
HierarchicalClustering
  LINKAGES : ArrayCollection
[static]
HierarchicalClustering
  LINKAGE_SINGLE : String = "Single"
[static]
HierarchicalClustering
Method detail
averageLinkage()method
public static function averageLinkage(distance:Array, cluster1:Array, cluster2:Array):NumberParameters
distance:Array
 
cluster1:Array
 
cluster2:Array

Returns
Number
cluster()method 
public static function cluster(distance:Array, linkage:String, optimizeLeafOrder:Boolean = true, clusters:Array = null, leafOrder:Array = null):Object

hierarchical agglomerative clustering (Eisen et al, 1998).

Parameters
distance:Array
 
linkage:String
 
optimizeLeafOrder:Boolean (default = true)
 
clusters:Array (default = null)
 
leafOrder:Array (default = null)

Returns
Object
completeLinkage()method 
public static function completeLinkage(distance:Array, cluster1:Array, cluster2:Array):NumberParameters
distance:Array
 
cluster1:Array
 
cluster2:Array

Returns
Number
getLeafOrder()method 
public static function getLeafOrder(tree:Array):ArrayParameters
tree:Array

Returns
Array
getLeafPositions()method 
public static function getLeafPositions(tree:Array):ArrayParameters
tree:Array

Returns
Array
orderLeafs()method 
public static function orderLeafs(v:Array, S:Array):Object

optimal leaf ordering (Bar-Joseph et al, 2001)

Parameters
v:Array
 
S:Array

Returns
Object
pairwiseDistance()method 
public static function pairwiseDistance(vector1:Array, vector2:Array, metric:String, p:Number = 1):Number

pairwise distance

Parameters
vector1:Array
 
vector2:Array
 
metric:String
 
p:Number (default = 1)

Returns
Number
printTree()method 
public static function printTree(tree:Array):StringParameters
tree:Array

Returns
String
reverseTree()method 
public static function reverseTree(tree:Array):ArrayParameters
tree:Array

Returns
Array
singleLinkage()method 
public static function singleLinkage(distance:Array, cluster1:Array, cluster2:Array):NumberParameters
distance:Array
 
cluster1:Array
 
cluster2:Array

Returns
Number
Constant detail
DISTANCE_METRIC_CHEBYCHEVconstant
public static const DISTANCE_METRIC_CHEBYCHEV:String = "Chebychev"
DISTANCE_METRIC_CITYBLOCKconstant 
public static const DISTANCE_METRIC_CITYBLOCK:String = "City Block"
DISTANCE_METRIC_CORRELATIONconstant 
public static const DISTANCE_METRIC_CORRELATION:String = "Correlation"
DISTANCE_METRIC_COSINEconstant 
public static const DISTANCE_METRIC_COSINE:String = "Cosine"
DISTANCE_METRIC_EUCLIDEANconstant 
public static const DISTANCE_METRIC_EUCLIDEAN:String = "Euclidean"
DISTANCE_METRIC_HAMMINGconstant 
public static const DISTANCE_METRIC_HAMMING:String = "Hamming"
DISTANCE_METRIC_JACCARDconstant 
public static const DISTANCE_METRIC_JACCARD:String = "Jaccard"
DISTANCE_METRIC_MINKOWSKIconstant 
public static const DISTANCE_METRIC_MINKOWSKI:String = "Minkowski"
DISTANCE_METRICSconstant 
public static const DISTANCE_METRICS:ArrayCollection
LINKAGE_AVERAGEconstant 
public static const LINKAGE_AVERAGE:String = "Average"
LINKAGE_COMPLETEconstant 
public static const LINKAGE_COMPLETE:String = "Complete"
LINKAGESconstant 
public static const LINKAGES:ArrayCollection
LINKAGE_SINGLEconstant 
public static const LINKAGE_SINGLE:String = "Single"