I want to color my clusters with a color map that I made in the form of a dictionary (i.e. {leaf: color}). I've tried following https://joernhees.de/blog/2015/08/26/scipy-hierarchical-clustering-...

I want to use hierarchical cluster analysis to get the optimal number (K) of clusters automatically, then apply this K to K-means clustering in python. After studying many article, I know some me...

I have a set of genes which have been aligned and clustered based on DNA sequences, and I have this set of genes in a Newick tree representation (https://en.wikipedia.org/wiki/Newick_format). Does ...

(This post is continuation of my previous question on divisive hierarchical clustering algorithm.) The problem is how to implement this algorithm in Python (or any other language). Algorithm desc...

Is is possible to select the number of clusters in the HDBSCAN algorithm in python? Or the only way is to play around with the input parameters such as alpha, min_cluster_size? Thanks UPDATE: her...

I'm confused about the difference between the following parameters in HDBSCAN min_cluster_size min_samples cluster_selection_epsilon Correct me if I'm wrong. For min_samples, if it is set to 7, t...

I am trying to create program that cluster documents using hierarchical agglomerative clustering, and the output of the program depends on cutting the dendrogram at such a level that I get maximum ...

Have anyone heard about any package or functionality that works the same as the dist{stats} function from R which creates the distance matrix that is computed by using the specified distance me...

I'm trying to learn how to use dendrograms in Python using SciPy . I want to get clusters and be able to visualize them; I heard hierarchical clustering and dendrograms are the best way. How can ...

I have a matrix data, and want to visualize it with heatmap. The rows are species, so I want visualize the phylogenetic tree aside the rows and reorder the rows of the heatmap according the tree. I...

Given a distance matrix, with similarity between various professors : prof1 prof2 prof3 prof1 0 0.8 0.9 prof2 0.8 0 0.2 prof3 0.9 0.2 0 I need to perform hierarchical clustering on this data...

I created a heatmap based on spearman's correlation matrix using seaborn clustermap as folowing: I want to paint the dendrogram. I want the dendrogram to look like this: dendrogram but on the heatm...

In order to clusterize a set of time series I'm looking for a smart distance metric. I've tried some well known metric but no one fits to my case. ex: Let's assume that my cluster algorithm extra...

So I am using fastcluster with SciPy to do agglomerative clustering. I can do dendrogram to get the dendrogram for the clustering. I can do fcluster(Z, sqrt(D.max()), 'distance') to get a pretty go...

I want to cluster Javascript objects by one of their string key values (description). I already tried multiple solutions and would like some guidance on how to approach the problem. What I want: L...

I am using hierarchical clustering from seaborn.clustermap to cluster my data. This works fine to nicely visualize the clusters in a heatmap. However, now I would like to extract all row values tha...

I'm making a clustered map with mapbox supercluster. The problem I face is that clusters are not at the correct location. For example I only have dogs in the netherlands but when zoomed out they ar...

I work on hierarchical agglomerative clustering on large amounts of multidimensional vectors, and I noticed that the biggest bottleneck is the construction of the distance matrix. A naive implement...

I have a large (106x106) correlation matrix in pandas with the following structure: +---+-------------------+------------------+------------------+------------------+------------------+-----------...

I have a numpy text file array at: https://github.com/alvations/anythingyouwant/blob/master/WN_food.matrix It's a distance matrix between terms and each other, my list of terms are as such: http:/...

My objective is to cluster words based on how similar they are with respect to a corpus of text documents. I have computed Jaccard Similarity between every pair of words. In other words, I have a s...

I'm trying to use agglomerative clustering with a custom distance metric (ie affinity) since I'd like to cluster a sequence of integers by sequence similarity and not something like the euclidean d...

I am looking for a clustering dataset with "ground truth" labels for some known natural clustering, preferably with high dimensionality. I found some good candidates here (http://cs.joensuu.fi/sip...

Here is my resulting plot below but I would like it to look like the truncated dendrograms in astrodendro such as this: There is also a really cool looking dendrogram from this paper that I woul...

How do I draw a line in a dendrogram that corresponds the best K for a given criteria? Like this: Lets suppose that this is my dendrogram, and the best K is 4. data("mtcars") myDend <- as.d...