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

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Community detection and modularity

I am reading the book "Network science" of Barabasi and in particular the chapter on community detection. If I understand correctly, modularity is a goodness factor of partition calculated by a ...
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How to visualize simplified dendrograms of many samples in R

I want to make sense out of my samples by visualizing my hierarchical clustering of a large dataset into a dendrogram in R. However as I have over 450k samples, I cannot make any sense out of the ...
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merge small clusters in R [closed]

In R, I have cut a dendrogram into clusters. However some of the clusters have only few samples. How can I merge the small clusters with nearest big cuter. ...
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A high cophenetic correlation coefficient but dendrogram seems bad

I have 2 results for the same dataset. One is hierarchical clustering using Ward's method and I got 0.75 cophenetic correlation coefficient. The second is average method and I got 0.91 cophenetic ...
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33 views

Dendrogram for classification tree

I wonder if there any way to better visualize multiclass (~10) classification tree in MATLAB. The only solution I came up with is to use: ...
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70 views

How to interpret the numeric values for “height” using wards clustering method

I am a biology student investigating a new method of creating a dichotomous identification key. I have created a dendrogram using data I have collected from a survey on how people rate how similar ...
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Cluster similarity matrix as energies

I have a symmetric score matrix and I would like to cluster the values in two dimensions rather than through a tree. Is there any method / library that would take the input matrix and treat the scores ...
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1answer
53 views

How to specify K cluster in Hierarchical clustering with noisy data?

I'm new in Mining and Clustering and I wonder how to cut off the hierarchical clustering Dendrogram to obtain a specific number of clusters. The problem is here that the data is noisy and the ...
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How many clusters would you divide this dendrogram into?

I'm struggling as to where to cut this dendrogram: any help would be appreciated. Thanks
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Get k most diverse objects from dendrogram (hierarchical clustering)

I have a dendrogram which groups similar object in a hierarchical order. The problem I try to solve is based on a dendrogram how to get k most diverse objects. E.g. We start with some random (?) ...
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Structural Stability of Hierarchical Clustering

I am interested in some papers and reports about analysing the following problem: Assume, we have a stream of objects and a defined similarity/distance measure to calculate similarity/distance between ...
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596 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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254 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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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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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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1answer
221 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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1answer
4k views

Comparing hierarchical clustering dendrograms obtained by different distances & methods

[The initial title "Measurement of similarity for hierarchical clustering trees" was later changed by @ttnphns to better reflect the topic] I am performing a number of hierarchical cluster analyses ...
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280 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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449 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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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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1answer
289 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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1answer
718 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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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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156 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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2k 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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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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434 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?