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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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Extract distances from hclust (hierarchical clustering) object

I would like to calculate how good the fit of my cluster analysis solution for the actual distance scores is. To do that, I need to extract the distance between the stimuli I am clustering. I know that when looking at the dendrogram I can extract…
Esther
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Cutting a dendrogram in R

I am trying to cut this dendrogram into 3 groups: (T24, T1, T17, etc.), (T12, T15, T6, etc.) and (T2, T8, T3, T9) I have tried using cutree(hc, k=3, h=400) , but it continues to make the same groups. Any help is greatly appreciated. Here is my…
derp4herps
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R cut dendrogram into groups with minimum size

Is there an easy way to calculate lowest value of h in cut that produces groupings of a given minimum size? In this example, if I wanted clusters with at least ten members each, I should go with h = 3.80: # using iris data simply for reproducible…
C8H10N4O2
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How to color a dendrogram's labels according to defined groups? (in R)

I have a numeric matrix in R with 24 rows and 10,000 columns. The row names of this matrix are basically file names from which I have read the data corresponding to each of the 24 rows. Apart from this I have a separate factor list with 24 entires,…
novicegeek
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Error in plot.new() when creating PDF in R

When plotting a dendrogram in R, I get a funny error that I've never seen before. Error in plot.new() : cannot open file 'C:\Users\Sun\AppData\Local\Temp\RtmpKSRNuD\pdf12207aa37548', reason No such file or directory I didn't have that error…
madkitty
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Generating dendrograms from genealogy data in R

Is there any way to generate a dendrogram where each level of the graph represents a generation and only sons of the same father are connected at each level? I'm attempting to use R's hclust and plot functions to generate a dendrogram of father-son…
mattrepl
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Pretty dendrograms in R?

My dendrograms are horribly ugly, on the verge of unreadable, and usually look like this: library(TraMineR) library(cluster) data(biofam) lab <- c("P","L","M","LM","C","LC","LMC","D") biofam.seq <- seqdef(biofam[1:500,10:25], states=lab) ccost <-…
histelheim
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ylim in hclust plot

I have this simple code to draw a dendrogram but the feature ylim seems not to work. So no matter what I set it to it has a y range of [0,0.5] when drawn. Should I use another parameter for setting the ylim when drawing…
hora
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Plot horizontal dendrogram with hanging leaves? (R)

I would like to create a dendrogram plot with horizontal labels, but having the leaves hang according to their height, instead of just drop to the edge of the plot. Example: par(mfrow = c(1,2)) hc <- hclust(dist(USArrests), "ave") plot(hc) # a plot…
Tal Galili
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Generating a heatmap that depicts the clusters in a dataset using hierarchical clustering in R

I am trying to take my dataset which is made up of protein dna interaction, cluster the data and generate a heatmap that displays the resulting data such that the data looks clustered with the clusters lining up on the diagonal. I am able to…
Alos
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Exporting dendrogram as table in R

I would like to export an hclust-dendrogram from R into a data table in order to subsequently import it into another ("home-made") software. str(unclass(fit)) provides a text overview for the dendrogram, but what I'm looking for is really a numeric…
AnjaM
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Matching up the output of scipy linkage() and dendrogram()

I'm drawing dendrograms from scratch using the Z and P outputs of code like the following (see below for a fuller example): Z = scipy.cluster.hierarchy.linkage(...) P = scipy.cluster.hierarchy.dendrogram(Z, ..., no_plot=True) and in order to do…
nicolaskruchten
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How do I label the terminal nodes of a cut dendrogram?

I used the following code to cut the dendrogram at a particular height.The problem I'm having is that when I cut a dendrogram, I can't figure out how to add labels to the nodes.How can I cut a dendrogram with labels using R…
akash
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Problem with margins using plot function with as.dendrogram object

I'm trying to customize a clustering plot using both base R functions and the package "dendextend". Firstly I generate a cluster with the common hclust() function. Then I'm using "dendextend" to color the branches defined by k=groups. Then I'm using…
Vitorleo.ar
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How can i plot a truncated dendrogram plot using plotly?

I want to plot a dendrogram plot for hierarchical clustering using plotly and show a small subset of the plot as with the large number of samples the plot can be very dense at the bottom. I have plotted the plot using the plotly wrapper function…
Albin
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