Questions tagged [dendrogram]

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

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38 views

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 ...
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32 views

Interpreting the Bk plot in dendextend

So I am trying to compare two hierarchical clusterings of 25 variables. One is my from my "control" population and the other is from a "treated" population and I am trying to see if these populations ...
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23 views

Interpreting the Bk plot in dendextend

So I am trying to compare two hierarchical clusterings of 25 variables. One is my from my "control" population and the other is from a "treated" population and I am trying to see if these populations ...
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11 views

Dendrogram from Procrustean Multiple Factor Analysis

I was wondering if it was possible to create a dendrogram showing similar groups (hierarchical clusters) from the output of a Procrustean Multiple Factor Analysis. I have created some dummy data and ...
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34 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 ...
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65 views

Ward's method for calculating linkage

I have this points in 1d: $$x_1 = 1$$ $$x_2 = 1.5$$ $$x_3 = 3$$ $$x_4 = 4.5$$ $$x_5 = 8$$ $$x_6 = 9$$ And I need to do a dendrogram by hand using Ward distance. I wanted to verify my results so I ...
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20 views

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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831 views

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: ...
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637 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 ...
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229 views

Dendrogram y-axis labeling confusion

I have a large (106x106) correlation matrix in pandas with the following structure: ...
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42 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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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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807 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 ...
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1answer
155 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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131 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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135 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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325 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 ...
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1answer
204 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, ...
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879 views

Distance between two clusters

I have this distances: ...
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344 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 ...
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1answer
244 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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Step-by-step: Ward's method for calculating linkage

I'm trying to use Ward's method to calculate linkage for hierarchical agglomerative clustering with the data points below: $$a=(0,0)$$ $$b=(1,2)$$ $$c=(3,4)$$ $$d=(4,1)$...
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2answers
2k views

Applying Ward's method for calculating linkage

For an assignment, I have used iPython to create the dendrogram below, using Ward's method and Euclidean distance, from the following data: $$a=(0,0)$$ $$b=(1,2)$$ $$c=(3,4)$$ $$d=(4,1)$$ $$e=(2,2)$$ ...
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423 views

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 ...
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1answer
2k views

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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491 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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1k views

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 ...
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1answer
1k views

Centroid linkage clustering with hclust yields wrong dendrogram?

Let's look at this example: ...
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306 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 <...
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1answer
3k views

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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4k views

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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1answer
2k views

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 ...
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3answers
198 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 ...
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1answer
303 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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408 views

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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196 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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614 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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1answer
3k 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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1answer
1k 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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69 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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4k 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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1answer
695 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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91k views

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 (...
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21k 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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1answer
443 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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117 views

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 ...
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1answer
1k 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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1answer
1k 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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1answer
3k 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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692 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 ...