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Questions tagged [hclust]

R function from {stats} package - hierarchical cluster analysis on a set of dissimilarities and methods for analyzing it.

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how to find & label centroids of clusters created by hclust() in R?

I read the thread there but in this thread, the answer is saying using the column means for the cluster i (so if I have 3 clusters in total, i = 1,2,3; and if I have 2 clusters overall, i = 1,2). I will copy and paste their answers here: clusters =…
alwaysaskingquestions
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R - Isolate clusters with specific characteristics in hclust

I've used hclust to generate a cluster dendrogram of some data, but I need to isolate all the paired clusters, i.e. all the clusters that comprise just 2 pieces of data (the first ones to be clustered together), even if they might be clustered with…
Rquestion550
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match and add the cluster number to the original data

I am using the regular method to do a Hierarchical Clustering project. mydata.dtm <- TermDocumentMatrix(mydata.corpus) mydata.dtm2 <- removeSparseTerms(mydata.dtm, sparse=0.98) mydata.df <- as.data.frame(inspect(mydata.dtm2)) mydata.df.scale <-…
janicebaratheon
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How to use hclust() in R when dataset has NA values

How can I use hclust() in R when the dataset I am using has NA values? This is the function I have set up: data2 = apply(data,2, as.numeric) data2.hclust = hclust(data2, method='median') When I attempt this I receive this error message: Error in if…
bubbalouie
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how to transform the following similarity matrix to distance matrix for performing hclust?

I am trying to cluster nodes (C1, C2, C3...) of a graph using hclust and my similarity metric is number of links between nodes. I have data like c = matrix( c(0,1,3,1,0,5,3,5,0), nrow=3, ncol=3) Basically this is a similarity matrix C1 C2 …
rk567
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Subsets of a dataset as separate dendrograms, but in the same plot

I know I can plot a dendrogram as follows library(cluster) d <- mtcars d[,8:11] <- lapply(d[,8:11], as.factor) gdist <- daisy(d, metric = c("gower"), stand = FALSE) dendro <- hclust(gdist, method = "average") plot(as.dendrogram(dendro)) However I…
Crops
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Get names of specific members of clusters of heatmap() function R

Once you generate a heat map using 'heatmap()' function in R, is there a way to focus in and extract the members of a specific cluster? I have a heat map of 4500 x 420 members and it would be useful. Thanks.
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How to print the order of hierarchical clustering in R?

Using the following matrix of distances between 6 Italian cities: 0 662 877 255 412 996 662 0 295 468 268 400 877 295 0 754 564 138 255 468 754 0 219 869 412 268 564 219 0 669 996 400 138 869 669 0 Will R output the order of which it…
user2679447
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Adding labels to a dendrogram in ggplot using ggdendro in r

How can I add labels to a ggdendro plot? I realise from reading ?dendro_data that I am suppose to use the the call 'labels' but can't find an example of actual implementation. Could anybody please demonstrate how to add leaf labels to the example…
Elizabeth
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Extracting the tree structure in text from hclust in R

In the scope of a demand forecasting project, I would like to determine the best way to group time series that have similarity with each other so I can apply a Top Down forecasting algorithm. At the moment, my key question is to determine what are…
Jochem
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How do I save SVG plots from Databricks in R?

I have the following R code which I can run in R Studio to generate a CDH dendogram plot and save it locally as a SVG. c1 <- hclust(as.dist(subs_matrix), method = "ward.D2") #ward.D2 #scale the branches of the tree, only changes the aesthetics the…
Sam Eley
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How to get the new hclust object after using cutree function in R

How do I get the new hclust object after using cutree function? I know the standard output from cutree is a numerical vector that tells you the clusters each leaf node belongs. However, how can we get the aggregated tree structure after cutting at a…
Jiadong Fang
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How to replace dendrogram labels using only base R and/or ggplot2 packages?

I want to perform dendrogram visualization using hierarchical grouping with Minkowski method on my dataset from eurostat library. I want to make values shown in this dendrogram: to display country names like in this one I can only use base R…
Radeq2137
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Bootstrapped hclust with real data

I have a dataset with multiple observations for each category: country PC1 PC2 PC3 PC4 PC5 BD 0.0960408090569664 0.373740208940467 -0.369920989335273 -1.02993010449105 -0.481901935725247 BD -0.538617581045194 0.537010643603669 …
Shakir
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Collapsing an internal node in a dendrogram in R

I have a dendrogram produced by hclust in R. I want to collapse one internal node and get the resulting new hclust object (for plotting etc). Note that I'm not doing a horizontal cut but just collapsing one node. Thanks! I've looked through the…
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