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Questions tagged [dendrogram]

A dendrogram (or tree diagram) is a graph used to represent relationships in hierarchical clustering.

Tag usage

Questions on tag should be about implementation and programming problems, not about the statistical or theoretical properties of the technique.
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586 questions
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D3 Dendrogram - Not shown

I'm trying to work with a Dendrogram from the D3 library. I understand the example as far, but I can't see anything while viewing the file in the browser. It's just a white screen. Can someone help me how to show the figure? Or do you need further…
Johannes
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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 heatmap underlying data frame

I made a heatmap for which I ordered the rows and columns manually by their respective dendrograms. Is there a way to save the underlying data frame of the resulting heatmap which has been reordered? If it helps, Here is the code for the heatmap I…
Nitro
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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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In scipy.cluster.hierarchy.dendrogram, setting 'ax' or 'above_threshold_color' throws an unexpected keyword error

I'm using scipy 0.16.0 on a Windows 8.1 machine and getting an unexpected keyword error when I try to run the dendrogram() function from scipy with passed settings for 'ax' or 'above_threshold_color'. Here's the error: TypeError: dendrogram() got an…
Alex
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How to color specific elements when using plot() in R?

I recently learned how to make clustering plots in R, as detailed in my question found: here. So now I can make helpful plots, but there is one formatting feature that would really help... to be able to specify predefined groups of samples to be…
jake9115
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How to make heatmap of half triangled correlation matrix containing colored dendrogram?

I have a ranked correlation matrix. I wanted to visualize the half triangled correlation matrix with colored dendrogram heatmap.2 function of "gplots", where I failed because I do not know how to do it. then I tried R packages "corrgram" and…
Manvendra Singh
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Create dendrogram using an index (proportion data) as grouping variable, R

I want to create a dendrogram using an index (proportion data) that will show similar clusters. I am trying to decide what distance/similarity metric I have to use so that they represent the original index values. I have a data frame that looks…
user1626688
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hierarchical clustering in MapReduce to implement a dendrogram of representative link communities

I want to use hierarchical clustering with a similarity between links to build a dendrogram where each leaf is a link from the original network and branches represent link communities using hierarchical clustering in MapReduce. Any references…
Chris Rigano
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Structuring Plain Text to JSON

I am attempting to take a collection of strings, tokenize the strings into individual characters, and restructure them into JSON for the purpose of building a cluster dendrogram visualization (sort of like this word tree, except for strings…
Jason Heppler
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grouping using dendrogram matlab

I have a matrix A composed by 4 vectors (columns) of 12 elements each A = [ 0 0 0 0; 0.0100 0.0100 0.0100 0; 0.3000 0.2700 0.2400 0.2400; 0.0400 0 0.0200 0.0200; 0.1900 …
gabboshow
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Adding images to leafs of dendrogram, instead of text in R

I'm trying to achieve a radial dendrogram, similar to the one below in R (see this post). However, instead of the text on the leafs, I'd like to have an image, for example: Any idea how I could go about this?
Omar Wagih
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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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d3.js dendrogram : binding old and new properties to the svg element

My understanding of d3 is currently rather limited and I am currently fiddling with a dendrogram example of D3.js. It can be found on several places: on this interactive version for example. When I implement it, all goes fine until you try to update…
Sleenee
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Mark igraph communities in dendPlot

I'm trying to plot a dendrogram of a community that was detected using fastgreedy.community, but I would like to have the branches labeled with the community number they correspond to. Is there any way to do this automatically?
user3133832
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