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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 associate cluster labels and dendrogram in the same order on a plot

I'm trying to associate my cluster labels to the corresponding dendrogram, the problem is that the dendrogram does not use the order i want, it's ordering the cluster from the left to the right... I've seen some other post like this one which is a…
D Prat
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Color branches of a dendrogram based on column in dataframe

I want to color the branches of a dendrogram based on the value in a column of a dataframe used in the hclust function. Before you mark this question as duplicate as was done in this question, which links to this question. Note that this was…
Matthew Snyder
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R: How to identify and label cluster groups in a dendrogram (created by hclust)?

I have used hclust to identify clusters in my data, and determine the nature of those clusters. The following is a very simplified version: gg <- c(1,2,4,3,3,15,16) hh <- c(1,10,3,10,10,18,16) z <- data.frame(gg,hh) means <- apply(z,2,mean) sds <-…
B.Kenobi
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Cluster labels are cut off on horizontal hclust dendrogram

I used hclust and as.dendogram to make a dendrogram, but when I rotate it to a horizontal orientation, the model names are cut off. How can I make sure that the plot shows the entire model names?
Milton Alves
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is there a way to preserve the clustering in a heatmap but reduce the number of observations?

I have data-set with 90 observations(rows) across 20 columns. I have generated a pretty neat heatmap which clusters my data in two groups with the package pheatmap. Although its not entirely clean but the two clusters of dendrogram pretty much…
ivivek_ngs
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dendextend: color_branches not working for certain hclust methods

I am using R dendextend package to plot hclust tree objects generated by each hclust method from hclust{stats}: "ward.D", "ward.D2", "single", "complete", "average" (= UPGMA), "mcquitty" (= WPGMA), "median" (= WPGMC) or "centroid" (= UPGMC). I…
Zach Roe
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rotating dendogram x axis label in R

I am giving the example data provided by hclust help: mds2 <- -cmdscale(UScitiesD) hcity.D <- hclust(UScitiesD, "ward.D") plot(hcity.D, hang=-1) When you plot this the site labels are vertical- which is appropriate for this example since they use…
Birdonawire
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Why results are different in hclust and heat map.2 using same clustering functions?

I'm trying to understand a bit more my data doing some clustering analysis. Using the same data, I've done first a hclust with this code: # Dissimilarity matrix df <-scale(m.sel) d <- dist(df, method = "euclidean") # Hierarchical clustering using…
Fabiola Fernández
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hcpc and hclust functions give different results for mixed classification

I started to do a hierarchical classification on mixed datas using "hclust". However, the results do not contain any details about the variables importance for each cluster. That's why I did a classification using "HCPC" which give all these…
tang
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R hclust height of final merge

When performing the hierarchical clustering in R with the hclust function. How do you know the height of the final merge? So to clarify with some R default data: hc <- hclust(dist(USArrests)) dendrogram1 = as.dendrogram(hc) plot(hc) Will result…
Sleenee
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How can I highlight specific labels in a dendrogram?

I made a cluster analysis using simple following code hc2 = hclust(dist(geno.imp)) pdf(file="file.pdf", width=50) plot(hc2,cex=0.2) dev.off() I want to highlight some of the specific leaves (not the nodes). I have the list of those leaves in a…
user3533677
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Interpreting the result of 'cutree' from hclust/heatmap.2

I have the following code that perform hiearchical clustering and plot them in heatmap. set.seed(538) # generate data y <- matrix(rnorm(50), 10, 5, dimnames=list(paste("g", 1:10, sep=""), paste("t", 1:5, sep=""))) # the actual data is much larger…
neversaint
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Consensus tree or "bootstrap proportions" from multiple hclust objects

I have a list of hclust objects resulting from slight variations in one variable (for calculating the distance matrix) now I would like to make a consensus tree from this list. Is there a generic package to do this? I am hacking my way…
user198711
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Assign a cluster to an object in R

What's the easiest way to assign a cluster to a group in R? The functions utilized are: hclust and cutree. Basically, I want to assign one of the clusters created under cutree to an object. Thanks!
user2105555
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Does there already exist an R package that can print any list to the console as a tree (using ASCII symbols)?

I would find it convenient to be able to print out any list-mode R object using the same format as str.dendrogram. I wrote my own function that kind of works, but there's no point in duplicating effort. So, does anybody know of any packages that…
bokov
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