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Visualize cluster distances in DendrogramPlot


I want to perform a cluster analysis using the HierarchicalClustering package. Is there a way to display the inter-cluster distances in a dendrogram plot?



An example how the result should look like: here.



Answer



DendrogramPlot accepts Axes as an option. Despite syntax highlighting in red of Axes and AxesOrigin, GridLines etc. these options seem to work with DendrogramPlot.


Inter-cluster distance in a Cluster object is given as the third element.


enter image description here


Several combinations of DistanceFunction and Linkage where inter-cluster distances are highlighted in red and shown as green gridlines in the dendogram plot:


Needs["HierarchicalClustering`"]

Grid[{{ToString@#[[1]] <> "--" <> #[[2]]}, 
  {Replace[ Agglomerate[{1, 2, 10, 4, 8},

    DistanceFunction -> #[[1]], Linkage -> #[[2]]], 
    Cluster[a_, b_, c_, d__] -> 
    Cluster[a, b, Style[c, 18, Red, Bold], d], {0, 
    Infinity}]}, {DendrogramPlot[{1, 2, 10, 4, 8},
   DistanceFunction -> #[[1]], Linkage -> #[[2]], 
   LeafLabels -> (# &), 
   GridLines -> {None, Cases[Agglomerate[{1, 2, 10, 4, 8},
       DistanceFunction -> #[[1]], Linkage -> #[[2]]], 
      Cluster[a_, b_, c_, d__] :> c, {0, Infinity}]}, 
   GridLinesStyle -> Green, ImageSize -> 500, 

   Axes -> {False, True}, AxesOrigin -> {.75, Automatic}]}}] & /@ 
 Tuples[{{Automatic, ManhattanDistance}, {"Complete",  "Centroid"}}] // Column

enter image description here


So ... vertical axis does indeed measure the inter-cluster distances for a given DistanceFunction and Linkage.


For various combinations of DistanceFunction and Linkage you get the following pictures:


{#, Agglomerate[{1, 2, 10, 4, 8}, DistanceFunction -> Automatic, Linkage -> #], 
 DendrogramPlot[{1, 2, 10, 4, 8},
 DistanceFunction -> Automatic, Linkage -> #, 
 Axes -> {False, True}, AxesOrigin -> {-1, Automatic}],

 Agglomerate[{1, 2, 10, 4, 8}, DistanceFunction -> ManhattanDistance, Linkage -> #],
 DendrogramPlot[{1, 2, 10, 4, 8},
 DistanceFunction -> ManhattanDistance, Linkage -> #, 
 Axes -> {False, True}, AxesOrigin -> {-1, Automatic}]} & /@
 {"Single", "Average","Complete", "WeightedAverage", "Centroid", "Median","Ward"} // 
 Grid[Prepend[#, {"", "EuclideanDistance-Clusters", 
 "EuclideanDistance-Dendogram", "ManhattanDistance-Clusters",
 "ManhattanDistance-Dendogram"}], 
  Dividers -> All, Alignment -> Bottom] &


enter image description here


EDIT: What I get for Frederik's example in the comments:


DendrogramPlot[Prime[#] & /@ Range[30], Axes -> {False, True}, 
AxesOrigin -> {-1, Automatic}]

enter image description here


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