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resolving specific clusters from data (spectral clustering)

I'm trying to cluster this genetic data but even with multiple different methods k-means/medoids spectral, etc... I can't seem to resolve the two big clusters. Any suggestions? I would really like to be able to identify that central cluster around y=1. The goal is to run this on multiple datasets. enter image description here

clustering
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updated by Mensur Dlakic Mensur Dlakic • written by benformatics benformatics

What is x and y? What kind of data is that? Did you try a graph-based clustering based on these two dimensions? So building a KNN/SNN graph first and then cluster that with igraph (e.g. louvain)?

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written by ATpoint ATpoint

I like your suggestions, I will try that. It's gene coverage at specific coordinates.

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written by benformatics benformatics

1 answer

I think Gaussian mixture models will work well on this type of scatter, though you will likely end up with more than two clusters. If you provide [X, Y] coordinates for data points, I could tell you for sure.

You could literally plug in your data into a script below instead of random points they generate:

https://scikit-learn.org/stable/auto_examples/mixture/plot_gmm.html

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written by Mensur Dlakic Mensur Dlakic

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