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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 convert data.frame into distance matrix for hierarchical clustering?

I have a data frame defined in a format of distance matrix: > df DA DB DC DD DB 0.39 NA NA NA DC 0.44 0.35 NA NA DD 0.30 0.48 0.32 NA DE 0.50 0.80 0.91 0.7 I want to use it as distance matrix in hclust function. But when I try…
umair durrani
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How to plot an nmds with coloured/symbol points based on SIMPROF

Hi so i am trying to plot my nmds of a assemblage data which is in a bray-curtis dissimilarity matrix in R. I have been able to apply ordielipse(),ordihull() and even change the colours based on group factors created by cutree() of a hclst() e.g…
Lmm
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The 'height' component of 'tree' is not sorted Error in cutree

I am trying to do some grouping and am encountering this error. Evaluation error: the 'height' component of 'tree' is not sorted (increasingly). My input is: library(stringdist) name <-…
Ravonrip
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ANOSIM with cutree groupings

What i would like to do is an ANOSIM of defined groupings in some assemblage data to see whether the groupings are significantly different from one another, in a similar fashion to this example code: data(dune) data(dune.env) dune.dist <-…
Lmm
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cor_cophenetic behavior in randomizations

I am working in R, with the dendextend package, trying to compare hclusts objects with cop_cophenetic. I have two objects that rise from clustering: clusts and clusts1, and I want to compare the cophenetic correlation between them. I have a few…
erezgrn
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What is the difference between segments(from segmentation) and classes( from Hierchical Clustering)

I am working on meanshift segmentation using R! I am now abit confused!my first question is how I can cluster the segmentation file( defining each segment as a super pixel) and second how I can then define that how many objects and how many classes…
Oumnia Asadian
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hclust, dist in R explained methods for clustering words

I'm working with some tweet data using the twitter API and OAUTH. I am making a cluster dendrogram to cluster words used in 500 tweets. I am not exactly sure how the hclust function is clustering the words. i.e by what rules I need some logic…
CodeHawk
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Get the cut heights using identify.hclust()

I am manually cutting a dendrogram created from hclust in R using identify.hclust. The default return of the function is the IDs of observations in each group. I need this information, but I also need to know the height of this group. Is there any…
Oligg
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plot a very large data with many zeros

This is a small portion of a vey big data df<- structure(list(A = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.68906, 0, 0, 0, 0, 0, 0, 0, 0, 0.13597, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), B = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,…
user 127354
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How to cut a dendrogram in r

Okay so I'm sure this has been asked before but I can't find a nice answer anywhere after many hours of searching. I have some data, I run a classification then I make a dendrogram. The problem has to do with aesthetics, specifically; (1) how to cut…
Tzac
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Use hclust on upper triangle in R

I have a matrix like so: a b c a 1 3 4 b 3 1 2 c 4 2 1 Is it possible to use hclust on the upper triangle without splicing the matrix diagonally? structure(c(1, 3, 4, 3, 1, 2, 4, 2, 1), .Dim = c(3L, 3L), .Dimnames = list(c("a", "b", "c"), c("a",…
motiur
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How to adjust the color range in heatmap.2

I am trying to plot the heatmap using the R language. After plotting the heatmap graph, I found that the my heatmap was not appropriate for the interpretation because the range of the color key was not well adjusted. As you can see below, the color…
sclee1
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See distance matrix in each step of hclust

How can see distance matrix in any step of the hierarchical clustering algorithm(use hclust function in R)?
amin roshani
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r: Obtaining final cluster results in a table/ dataframe when using hclust()

I am conducting a hierarchical cluster analysis by using hclust() The code looks like this: hc <- hclust(dist(USArrests), "ave") Now, all I need is to get a table (or something equivalent) which contains all clusters and the observations (by their…
Jonathan Rhein
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How to export hclust cluster results

I'm new to R but I've been stuck on this issue for weeks now. I have a data set of 343 observations and 28 columns. The first of these 28 columns is an identifier. Before running my analysis, I omitted that ID column using newdata <- olddata[,2:28]…
1buzz
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