Questions on the R package dendextend
The dendextend R package includes functions and methods for extending dendrogram objects in R (visualization, manipulation and comparison).
Questions tagged [dendextend]
158 questions
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Dendrogram in R: how to properly hang branches (after coloring the labels)?
I have gone through other questions asked on this topic and have managed to "partially" get what I need. I want my dendrogram 's leaves to be color coded. Each leave represents a market and I have another column within my DF that tells what type of…
Batool
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Obtaining cluster hierarchy and nested cluster assignments
I am currently looking into hierarchy in the topics of documents. As a first step I find a vector representation of my documents, after which I use hierarchical clustering to determine whether there are topics within topics of the document. I want…
BDP1
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Setting lim in scale_y_reverse when plotting a ggdend object
I have dendrogram which I cut the branches of for a given depth cutoff. I then want to plot it using ggplot and limit the flipped y-axis:
set.seed(10)
mat <- matrix(rnorm(24*10,mean=1,sd=2),nrow=24,ncol=10)
dend <-…
dan
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How can I colour the nodes of a dendrogram as separate rows in R
I'd like to colour the nodes of a dendrogram at the bottom of the dendrogram - but in separate rows
This last dendrogram in the link below shows the nodes as coloured - however when its a big data set that one line gets very smeary
Label and color…
user3156942
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How to colour labels of a dendrogram by an additional factor in an independent data frame in R
I have a dendogram of 150 genes imported in R, and I have a data frame with the same labels of the dendogram with score values from 0 to 200, that are independent from the dendogram.
I would like to colour the labels of the dendogram with the score…
carolet
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R/Python: Heirarchical clustering, dendrogram annotation
I want to conduct a hierarchical clustering and plotting a classic dendrogram with a heatmap. This is reasonably easy using heatmap.2 or heatmap.3 in R, and seem reasonable easy in python as well. However, what I'm not really finding a nice solution…
Myggan
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R hclust -> dendrogram -> phylo?
I have hclust hierarchical cluster objects with hundreds of nodes and long labels. For example, synonyms of multiple genes within a family. See below.
I would like to cut the hclust into smaller subtrees and then visualize them with flexible…
Mark Miller
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selecting number of leaf nodes of dendrogram in heatmap.2 in R
In Matlab you can designate the number of nodes in a dendrogram that you wish to plot as part of the dendrogram function: dendrogram(tree,P) generates a dendrogram plot with no more than P leaf nodes.
My attempts to do the same with heatmap2 in R…
user3866594
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