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Questions tagged [pvclust]

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

31 questions
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R convert names to numbers

I have a data frame with donations and names of donors. **donation** **Donor** 25.00 Steve Smith 20.00 Jack Johnson 50.00 Mary Jackson ... ... I'm trying to do some…
screechOwl
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How to append bootstrapped values of cluster's (tree) nodes in NEWICK format in R

I want to make a tree (cluster) using Interactive Tree of Life web-based tool (iTOL). As an input file (or string) this tool uses Newick format which is a way of representing graph-theoretical trees with edge lengths using parentheses and commas.…
Newbie_R
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applying the pvclust R function to a precomputed dist object

I'm using R to perform an hierarchical clustering. As a first approach I used hclust and performed the following steps: I imported the distance matrix I used the as.dist function to transform it in a dist object I run hclust on the dist…
rlar
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Can someone explain the output from the pvclust function in R?

In the pvclust package in R, there is the pvclust() function. In the example provided in the function help file, there's the function: boston.pp <- pvpick(boston.pv) This is supposed to print out the clusters with high p-values. The output of this…
xyy
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Cluster analysis in R: How can I get deterministic results from pvclust?

pvclust is great for cluster analysis in R. However, when running it as part of a batch operation, it is annoying to get different results for the same data. Obviously, there are many "correct" clusterings of the same data, and it seems that pvclust…
Fabian Fagerholm
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Cluster Analysis using pvclust in R

I want to do cluster analysis of certain columns (variables), say var 5-var10. For that I used pvclust in R. Now, I want to add this column of clusters into the actual dataframe. Can anybody please help me to fix this problem. The code I used is…
Beta
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Cannot import pvclust by using rpy2 in python3.6 (Jupyter notebook)

I am using Jupyter notebook in anaconda and try to use the pvclust to perform hierarchical clustering on my data. My codes: from rpy2.robjects import r, pandas2ri from rpy2.robjects.packages import importr pandas2ri.activate() base =…
Ye Xu
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Drawing rectangles around specified labels in a dendrogram with 'dendextend'

I'm currently constructing a dendrogram and I'm using 'dendextend' to tweak the look of it. I've been able to do everything I want to (labelling leaves and highlighting branches of my chosen clusters), except drawing rectangles around pre-defined…
IsoBar
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pvclust on hclust generated dendrogram

I am interested in using the pvclust R package to determine significance of clusters that I have generated using the regular hierarchical clustering hclust function in R. I have a datamatrix that consists of ~ 8000 genes and their expression values…
user1876476
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Adding group information to pvclust dendrogram instead of sample name

This is what I'm doing mat <- read.table("Model_pvclust/Model18_FAB_M5_vs_M0_MAP_TF.txt",sep = "\t",strip.white = FALSE,check.names = FALSE,header=TRUE,row.names=1) drop <-…
PesKchan
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Function returning a plot not list of plots

I'm trying to run pvclust as a test Im running it in small subset of files. The issue is it works but instead of list which i would have used downstream to print it to individual files it gets printed. My code list_of_files <-…
PesKchan
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Hamming distance measure for pvclust

I am trying to create a Hamming distance measure for the pvclust clustering method. (There isn't one defined for this function.) I'm based on the example given for the cosine measure: cosine <- function(x) { x <- as.matrix(x) y <- t(x) %*% x res <-…
Avter
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View pvclust tree with many nodes in R

Is there any way to view hierarchical tree with too many nodes (around 10000+)? Changing the text size is not a viable option to see the labels at all. I tried converting to dendrogram and cut but the p-values disappear. I need to see the p-values…
Barry
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pvrect() rectangles in horizontal dendrogram (R)

I am trying to draw rectangles around clusters in a horizontal dendrogram. This works fine as long as I only cut the tree manually, e.g. dend<-as.dendrogram(hc) plot(dend, horiz=T) rect.dendrogram(dend, 3) However, I also want to highlight…
apeshifter
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can pvclust combine not variables,but obs. in R

Let's take it as example library("MASS") library("pvclust") result.par <- pvclust(Boston, nboot=1000, parallel=TRUE) plot(result.par) We see that pvclust combines variables. Is it possible to combine observation in clusters ie. i want output (with…
psysky
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