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Questions tagged [pvclust]

pvclust is an R package for assessing the uncertainty in hierarchical cluster analysis.

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How to extract node position from boot.hclust object (pvclust)?

I know I can obtain the au/bp number from the final object from pvclust, but I could not figure out which of the samples or edges are associated with it. What I am trying to do is to assign the au value to the samples. Thanks! data(lung) lung.pv <-…
SplitInf
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Change label dendrogram with pvclust in R

I am trying to get a cluster validation with pvclust following this example: result <- pvclust(mydata, method.dist = "euclidean", method.hclust = "ward.D2", nboot = 1000) Which seems to work fine. However, if I visualize the results…
Hannah H.
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How to use a different distance method (simpson) in pvclust

I am trying to run function pvclust, but using simpson dissimilarities instead using one of the default distances. Can I include a distance function inside the pvclust (method.dist). I already have my simpson dissimilarity intex as a dist. object…
Diego García Olaechea
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Error when using ''ward'' method with pvclust R package

I am having some troubles regarding a cluster analysis that I am trying to do with the pvclust package. Specifically, I have a data matrix composed by species (rows) and sampling stations (columns). I want to perform a CA in order to group my…
Marie-Christine Rufener
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Rewrite a function in locked env

Using pvclust::pvclust , I got an error Error in solve.default(crossprod(X, X/vv)) : Lapack routine dgesv: system is exactly singular: U[2,2] = 0 Calls: ... pvclust.merge -> lapply -> FUN -> msfit -> solve -> solve.default Execution…
Awawa
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bootstrapping own built function pvclust does not work

I am using sequence analyses methods in order to measure similarity between different "sequences of spatial use", represented as strings of characters. Here is a theoretical example with three classes (A: City, B: Agriculture, C: Mountain) for two…
jedgroev
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Extract significant subtrees/clusters from pvclust keeping its hierarchy

The following R code produces hierarchical cluster via multiscale bootstrap resampling in the Boston dataset. library(pvclust) library(MASS) data(Boston) boston.pv <- pvclust(Boston) boston.pp <- pvrect(boston.pv) clusters <-…
tbrittoborges
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cluster one-dimensional data using pvclust

Thanks for taking time read this question. I have some one-dimensional data to cluster in R. The basic hclust command works fine. But the pvclust command, however, does not take one-dimensional data, and keeps saying: Error in hclust(distance,…
Qiyun Zhu
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Return horizontally a dendrogram of the function [pvclust] on R

I would like to return a dendrogram of the [pvclust] function as above without losing the information (height, au value, bp value and edge value). This dendrogram To obtain this dendrogram with the information from the first dendrogram I tried the…
CM2
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Add hierarchical clustering to correlation plot?

I've generated correlation heatmaps using the following code: corrplot(data, method = "color", type = "lower", order = "hclust", col=colorRampPalette(c("blue","white","red"))(400), tl.col = 'black', cl.ratio = 0.2, tl.srt = 45) I also have…
LL21
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Adjust dendogram made by the pvclust package

I would like to improve my dendrogram that I made using the pvclust package. I am not able to see most AU / BP labels, as you can see in the image. Could you help me solve this ?. I would like to see all AU / BP labels for the dendrogram. Below is…
user13047398
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pvclust edit dendogram graph

I'm running some cluster analysis and I'm using pvclust as showed below: d.pv <- pvclust(t(mtcars), method = "euclidean", method.hclust = "complete", nboot = 10) plot(d.pv) I want to edit the graph and remove red, green numbers, and …
Al14
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Rotate leaf labels in pvclust dendrogram plot

I'm using the pvclust package in R to perform bootstrapped hierarchical clustering. The output is then plotted as a hclust object with a few extra features (different default title, p-values at nodes). I've attached a link to one of the plots…
JSneathThompson
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Converting a list into a named vector in R

I did a cluster analysis with the package pvclust on R. I extracted the resultant clusters components with the command "pvpick" resulting in a list with 8 clusters. [[1]] [1] "sco.plu" "tra.myo" [[2]] [1] "sya.pap" "syn.foe" "syn.int" [[3]] [1]…
Vinifonz
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Hierarchical Clustering in R - 'pvclust' Issues

I have made a reproducible example where I am having trouble with pvclust. My goal is to pick the ideal clusters in a hierarchal cluster dendogram. I've heard of 'pvclust' but can't figure out how to use it. Also if anyone has other suggestions…
analytics
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