A dendrogram (or tree diagram) is a graph used to represent relationships in hierarchical clustering.

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Pearson Correlation with symmetric pairs?

I am correlating two features in the leaves of a dendrogram for a given tree distance (2,3,...). When i find the pair "A-B" at distance x I will also have the duplicate "B-A" in the same set for ...
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63 views

Determine Number of Clusters Using Silhouette Method and Distance Matrix

I have a tree and its associated distance matrix. Now I want to cut the tree to give a desired number of clusters. Luckily there are a number of methods for determining the number of clusters as ...
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138 views

Cophenetic distance matrix to a dendrogram

In hierarchical clustering procedure, a distance matrix is used to construct a dendrogram with an appropriate method of clustering. In the process of constructing a dendrogram, a cophenetic matrix is ...
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59 views

Extract (ultrametric) distances from hclust or dendrogram

How can the matrix of (ultrametric) distances be extracted from the result of hclust (or a dendrogram in general) in R? The ...
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25 views

hypothesis testing in hierarchical trees

Suppose I have an hierarchical tree organising people according to their music preferences. Each person then has 3 extra properties A, B and C (e.g. parent's supportiveness on musical education). I ...
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442 views

How to plot Optics Clustering result in Matlab (reachability plot)

I modified the following script for Optics clustering ( http://chemometria.us.edu.pl/download/OPTICS.M ) in order to work with DTW distance instead than Euclidean's. I obtained the Order vector ...
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105 views

Leaf ordering for hierarchical clustering dendrogram

Assuming merging process was completed and we have the history of n-1 merged clusters (merge two clusters p and ...
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913 views

Measurement of similarity for hierarchical clustering trees

I am performing a number of hierarchical clusters on a dataframe of patient records (e.g. similar to http://www.biomedcentral.com/1471-2105/5/126/figure/F1?highres=y) I am experimenting with ...
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160 views

Which similarity coefficient should I use with Ward linkage?

I just attempted implementations of Ward linkage and UPGMA linkage, as well as Pearson and Euclid similarity coefficients. To my surprise, both similarity coefficients gave the same clustering with ...
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How to randomize the tips of a functional trait dendrogram?

I have generated a functional trait dendrogram using species x trait and plots x species matrices through dbFD in package FD. I want to randomize the tips of the ...
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258 views

How to convert a dendrogram back into a distance matrix?

Example code: our_dist <- dist(USArrests[1:4,]) dend <- as.dendrogram(hclust(our_dist , "ave")) plot(dend ) I would now wish to have a "dend2dist" function ...
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501 views

Does SPSS rescale dendrograms?

A colleague and I have been clustering some data in SPSS (v19) and R (2.15), respectively. Using the same distance metric and agglomeration method, we get identical merge orders/agglomeration ...
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2k views

Dendrograms using clustergram vs traditional ways in Matlab

Good Morning, By comparing the dendrograms produced by the clustergram object and the "manual" approach i.e. pdist -> linkage -> dendrogram I found they are different, but cannot find an explanation ...
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173 views

How can I weight certain factors more heavily when computing distance function?

I'm working on a "player phylogeny" to help make comparisons between potential NBA draft picks and current players. An example is shown below: I'm using the dist() function in R, and am assuming ...
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391 views

Cluster analysis in R produces reversals on dendrogram

I'm attempting to perform hierarchical agglomerative cluster analysis in R. However, when I use particular clustering methods, I get reversals (upward branching) in the resulting tree, which ...
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2answers
1k views

How to derive a distance function based on multiple variables for cluster analysis?

I am not a statistician, so please excuse my lack of statistics knowledge/terminology. I have bunch of network nodes that I want to run cluster analysis on and identify clusters. So as far as I ...
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143 views

How do I use cluster analysis in creating a model?

I have a training data set that I've done some cluster analysis on using R's pvclust package. I have a dendrogram of the results and am currently looking for the ...
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1k views

Anyone know of a simple dendrogram visualizer?

I've written a small hierarchical clustering algorithm (for better or for worse). I'd like a quick way of visualizing it, any tooling ideas?
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4k views

How to plot a fan (Polar) Dendrogram in R?

I'm referring to something like this: suggested dataset for showing a solutions: data(mtcars) plot(hclust(dist(mtcars)))
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Where to cut a dendrogram?

Hierarchical clustering can be represented by a dendrogram. Cutting a dendrogram at a certain level gives a set of clusters. Cutting at another level gives another set of clusters. How would you pick ...
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365 views

A measure to describe the distribution of a dendrogram

Could anyone suggest some statistical measures to describe the distribution of a dendrogram? If I have two dendrograms, how could can I quantify their structural differences?