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Questions tagged [dendrogram]

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

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Looking for a suitable way to find groups of events

I have an excel file in which I have three columns. The first one is the name of an event, the second one is the moment the event starts and the third one is the time at which an event ends. Let's say ...
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How to incorporate p-value information for pairwise distances into clustering?

Consider I have a $n \times n$ distance matrix I want to use for hierarchical clustering, where the distance metric I use ranges from 0-1. I also have a second $n \times n$ matrix that gives me the p-...
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Drawing a dendrogram based on a confusion matrix

I have a simple 2D confusion matrix that I normalised for every true class. Now, what would be the best method to visualise this as a dendrogram? I have seen hierarchical agglomerative clustering on ...
Damiaan Reijnaers's user avatar
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Is it possible changing y axis of dendrogram from height to similarity?

I made dendrogram based on species data of different sites using ward's method Chord transformation was applied and the (dis)similarity was calculated by vegan package Here is my question : Can I ...
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Why is the dendrogram structure different from what I see of my data in a 3D PCoA?

I conducted hierarchical clustering on a dissimilarity matrix computed from a series of species distribution models text and I seem to get different visible structure between the dendrogram and the 3D ...
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Calinski-Harabasz score as a validity index for hierarchical clustering with distance matrix

I have a distance matrix that I want to performed hierarchical clustering with, and find the optimal number of clusters by maximizing the Calinski-Harabasz (CH) score. However, I only know how to ...
user17298847's user avatar
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How to compare two dendrograms

I want to find a method to compare two dendrograms. I have documents that were read by some people and they made a dendrogram that indicates which documents they think are more similar. Now I want to ...
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Interpretation of the height of a dendrogram and intra/inter deviance corrispondence

I am practicing hierarchical clustering and I am having doubts about the interpretation of dendrogram height. Let's take the code in example with points (1,1), (2,2), (5,5), (9,9), (10,10), and (13,13)...
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Finding correlations between categories using Correlations matrix and heatmap with dendrogram

I have a dataset with 5000 obs grouped by category: 1: science 0.5: philosophy -0.5: medicine -1: law I would like to run some statistics to find correlations among variables within the groups, for ...
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Clustering multivariate binary data

I want to use a clustering algorithm which can catch the following within a multivariate binary dataset. In the sample below, since class 1 and 2 appear twice within column A and B they will form a ...
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Comparing cluserting structure of two datasets

I have two datasets, one with probands of a certain disease in it, the other has their siblings in it. Both of them contain the exact same variables (some phenotypes). Now, I would like to compare the ...
Courtney's user avatar
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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, ...
Ninjadog's user avatar
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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 ...
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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 ...
Cas Toyel's user avatar
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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 ...
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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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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 ...
Keith Hughitt's user avatar
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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: ...
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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 ...
Darren Christopher's user avatar
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Dendrogram y-axis labeling confusion

I have a large (106x106) correlation matrix in pandas with the following structure: ...
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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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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 ...
orange's user avatar
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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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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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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 ...
user1614062's user avatar
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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 ...
SriniShine's user avatar
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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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Distance between two clusters

I have this distances: ...
Gotey's user avatar
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2 answers
478 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 ...
Rodrigo's user avatar
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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 ...
Marina Oana's user avatar
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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)$...
Harr's user avatar
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2 answers
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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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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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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 (...
Pugl's user avatar
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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: ...
Samuel Lampa's user avatar
5 votes
1 answer
2k 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 ...
siler's user avatar
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1 answer
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Centroid linkage clustering with hclust yields wrong dendrogram?

Let's look at this example: ...
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490 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 <...
Pete's user avatar
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4 votes
1 answer
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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 ...
oipo's user avatar
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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 ...
Emrah Bilgiç's user avatar
3 votes
1 answer
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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 ...
radellin's user avatar
3 votes
3 answers
220 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 ...
El Dude's user avatar
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5 votes
2 answers
466 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 ...
farzad's user avatar
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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
Paul Jenkins's user avatar
4 votes
1 answer
306 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 (?) ...
Sebastian Widz's user avatar
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875 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 ...
Sebastian Widz's user avatar
2 votes
1 answer
5k 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 ...
Crops's user avatar
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3 votes
1 answer
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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 ...
Stats's user avatar
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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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