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Questions tagged [dendrogram]

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

Tag usage

Questions on tag should be about implementation and programming problems, not about the statistical or theoretical properties of the technique.
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586 questions
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How to plot scipy.hierarchy.dendrogram using polar coordinates?

I'm trying to adapt the following resources to this question: Python conversion between coordinates https://matplotlib.org/gallery/pie_and_polar_charts/polar_scatter.html I can't seem to get the coordinates to transfer the dendrogram shape over to…
O.rka
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Getting a node stack overflow error while trying to print a dendrogram

I'm trying to get the heights of internal nodes of a dendrogram in a BFS order. The utils::str function prints the dendrogram in a BFS order., so I thought I'd use that (redirect the output to a file and do some parsing on that to get the info I…
dan
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Dendrogram with Corrplot (R)

Does anyone have a method to adorn an R corrplot correlation plot with a dendrogram?
abalter
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How to visualize (dendrogram) a dictionary of hierarchical items?

This is my first time of doing visualization from hierarchical data in dictionary format with Python. Last part of the data looks like this: d = {^2820: [^391, ^1024], ^2821: [^759, 'w', ^118, ^51], ^2822: [^291, 'o'], ^2823: [^25, ^64], ^2824:…
MarkokraM
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How to change dendrogram labels in r

I have a dendrogram in R. It is based on hierachical clustering using hclust. I am colouring labels that are different in different colours, but when I try changing the labels of my dedrogram (to the rows of the dataframe the cluster is based on)…
sequence_hard
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How to colour the labels of a dendrogram by an additional factor variable in R

I have produced a dendrogram after running hierarchical clustering analysis in R using the below code. I am now trying to colour the labels according to another factor variable, which is saved as a vector. The closest that I have come to achieving…
jjulip
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Scipy dendrogram leaf label colours

Is it possible to assign colours to leaf labels of dendrogram plots from Scipy? I can't figure it out from the documentation. Here's what I've tried so far: from scipy.spatial.distance import pdist, squareform from scipy.cluster.hierarchy import…
herrfz
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Displaying TraMineR (R) dendrograms in text/table format

I use the following R code to generate a dendrogram (see attached picture) with labels based on TraMineR sequences: library(TraMineR) library(cluster) clusterward <- agnes(twitter.om, diss = TRUE, method = "ward") plot(clusterward, which.plots = 2,…
histelheim
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cluster presentation dendrogram alternative in r

I know dendrograms are quite popular. However if there are quite large number of observations and classes it hard to follow. However sometime I feel that there should be better way to present the same thing. I got an idea but do not know how to…
fprd
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Dendogram Coloring by groups

I created a heatmap based on spearman's correlation matrix using seaborn clustermap as folowing: I want to paint the dendrogram. I want the dendrogram to look like this: dendrogram but on the heatmap I created a dict of colors as folowing and got an…
Rotem Bartuv
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Plot the dendrogram of communities found by NetworkX Girvan-Newman algorithm

The Girvan-Newman algorithm for community detection in networks: detects communities by progressively removing edges from the original graph. The algorithm removes the “most valuable” edge, traditionally the edge with the highest betweenness…
Giora Simchoni
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Converting igraph to networkx for clustering

I have a python code which uses igraph library import igraph edge = [(0, 6), (0, 8), (0, 115), (0, 124), (0, 289), (0, 359), (0, 363), (6, 60), (6, 115), (6, 128), (6, 129), (6, 130), (6, 131), (6, 359), (6, 529), (8, 9), (8, 17), (8, 115)] G =…
Dgstah
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Change Dendrogram leaves

I want to modify the properties of the leaves in a dendrogram produced from plot of an hclust object. Minimally, I want to change the colors, but any help you can provide will be appreciated. I did try to google the answer, but but every solution…
Btibert3
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Visualize lowest nodes in hierarchical clustering with dendrogram

I'm using linkage to generate an agglomerative hierarchical clustering for a dataset of around 5000 instances. I want to visualize the 'bottom' merges in the hierarchy, that is, the nodes close to the leaves with the smallest distance measures.…
Cecilia
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Dendrogram edge (branch) colors to match tip (leaf) colors (ape package)

I'm trying to add color to the edges (lines) of a phylogeny-type plot in R using the plot.phylo command from the ape package. This example is for a "fan" type plot, though I expect the approach would be the same with a "phylogram type" or…
David Roberts
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