# Questions tagged [dendrogram]

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

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### Variables plotted weirdly in a dendrogram (ClustOfVar for R)

I plotted a dendrogram using plot(hclustervar(X.quali=data)) from the R package ClustOfVar because I wanted to explore the structure behind the survey responses. All variables were coded as factors, ...
1answer
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### How to interpret a hierarchical clustering dendrogram?

I have a machine learning code that predicts whether a gene is likely to cause disease (the model gives the gene a score somewhere between 0 and 1, with 1 being causal for the disease). The training ...
2answers
256 views

### Hierarchical clustering and Dendrogram interpretation

I'm quite new to cluster analysis and I was trying to perform a hierarchical clustering algorithm (in R) on my data to spot some groups in my dataset. Initially, I tried with the k-means, with the ...
1answer
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### Hotelling's $T^2$ test VS dendrogram

When i perform a Hotelling's $T^2$ test on a dataset, it stated that there is strong evidence that the mean vectors of the two groups differ. However, when I create a dendrogram, I got: where number ...
0answers
113 views

### Cutting dendrogram at certain point

I have a question about cutting dendrogram like that It shows some hierarchy in the prison I have to cut it to separate the group. Is it possible to cut not all dendrograph at the same height like ...
1answer
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### Quantifying non-random distribution of label across dendrogram / correlation matrix?

Overview Given a correlation matrix generated from $n$ observations, each of which is associated with one or categorical binary or multinomial labels, how can one quantify the (non-)random ...
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### Hierarchical clustering dendrogram on a distance matrix

When computing hierarchical clustering over a data matrix, a dissimilarity matrix is first computed in order to build the tree (dendrogram). For example: ...
1answer
1k views

### Dendrogram: Hierachical Clustering on Text data

I would like to use hierarchical clustering for my text data using sklearn.cluster library in Python. However, when I plot the dendrogram to inspect where I should ...
0answers
300 views

### Dendrogram y-axis labeling confusion

I have a large (106x106) correlation matrix in pandas with the following structure: ...
1answer
49 views

### R: What is the distance function equivalent for this formula?

Hi I'm using an R package that calculates distance with this formula here, as.dist(1 - cor(df, use = "pa")) However I cannot seem to find an equivalent dist ...
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2k views

### Hierarchical clustering in R - centroid linkage - problem with dendrogram heights

I have got a problem with understanding the hierarchical clustering algorythm, especially centroid linkage method. I have read many articles with description and they seems to be quite easy but I ...
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868 views

### Clustering correlated variables based on correlation matrix [duplicate]

I'm trying to group correlated variables together. I calculated the correlation matrix (Pearson correlation) and filtered out insignificantly correlated variables. What I'm left with is this ...
1answer
164 views

### Hierachical cluster analysis of ordinal variables?

I have a dataset containing 400 variables (chemical compounds, amount classes) with values 0,1,2, or 3 and 50 entries (species). Can I use hierarchical cluster analysis to get a dendrogram that ...
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153 views

### Algorithm to sort the elements in a way that allows drawing non-crossing dendrograms out of Hierarchical Clustering [closed]

I have written from scratch (with Fortran) my own implementation of the Ward algorithm to perform HC. The output of the program consists of two elements: a vector with the distance after each step, ...
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139 views

### Test if order of objects in hierarchical clustering is uniformly distributed

I have performed hierarchical clustering and am looking for a way to test if a specific set of objects (genes, in this case) are clustered together. From inspecting the output I cannot identify a ...
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365 views

### Visually comparing hierarchical clusterings

I'm working with a computational model. The model demonstrates the behaviour of a several sub metabolic systems (A, B, C, D, E, F, G, H, I and J) of a bacteria. I cluster these sub systems based on ...
1answer
207 views

### Heatmap based on gene expression trend [closed]

Can anybody guide me on the R code for the following problem? My data contains expression values of Genes A, B, C, D, E, F, G, H, and I in a time course study for two time steps, 48 and 72 hours, ...
1answer
972 views

### Distance between two clusters

I have this distances: ...
2answers
383 views

### Dendrogram from table with repeated lines

I have some data from mass spectrometry of some plant samples (11 morphospecies and 4 treatments for each). Each species/treatment yields a graphic like the one below. Each column in the graphic ...
1answer
291 views

### Would anyone be able to help me interpret the dendrogram in the picture?

The dendrogram was obtained using SPSS, the Nearest Neighbor method alongside the Squared Euclidian Distance. It groups together glass fragments from 3 different origins but I have difficulties with ...
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### Why does the heatmap of this gene expression data don't show a decent clustering here?

The heatmap has samples in columns and probesets/features in the rows. The genes are already selected based on a very low p-value threshold using 2 sample t-test on the two phenotypic subgroups of the ...
1answer
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### Dendrogram in Hybrid Hierarchical Clustering and Cut-off criterion (Calinski-Harabasz presently)

I have questions regarding the dendrogram and the cut-off related to hybrid hierarchical clustering performed on data, as depicted below and taken from this paper Questions regarding Panel A (...
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563 views

### Do heights between branches in R's heatmap dendrogram reflect true distances?

We are trying to interpret a heatmap that looks like this: ... and plotted with this plotting code: ...
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### Purpose of dendrogram and hierarchical clustering

This is likely a very naive question. I've lately been reading about hierarchical clustering algorithms, and various discussions about how to interpret dendrograms or find optimal heights for cutting ...
1answer
2k views

### Centroid linkage clustering with hclust yields wrong dendrogram?

Let's look at this example: ...
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388 views

### Hierarchical Cluster Analysis validation

I have never used Hierarchical Cluster Analysis for inferential statistics before, but the dendrogram it produces provides a nice way to visualise my data. I applied the HCA to my variables with the <...
1answer
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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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### 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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### How to interpret the numeric values for “height” in a dendrogram using Ward's 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 ...
3answers
205 views

### 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 ...
1answer
328 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
1answer
215 views

### 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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660 views

### 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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### 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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### 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 ...
0answers
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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 (...
1answer
736 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 ...
3answers
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### How to interpret the dendrogram of a hierarchical cluster analysis

Consider the R example below: plot( hclust(dist(USArrests), "ave") ) What exactly does the y-axis "Height" mean? Looking at North Carolina and California (...
1answer
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### 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 ...
1answer
467 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? [closed]

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 ...
1answer
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### 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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### 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 ...
1answer
735 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 that ...
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### 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 ...