Add custom clustering#11642
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- cluster_metrics: computes clustering quality metrics + k-sweep - cluster_viz: generates PCA, UMAP and t-SNE plots colored by cluster - Both use conda environment.yml - Full nf-test coverage
Co-authored-by: Jonathan Manning <pininforthefjords@gmail.com>
Co-authored-by: Jonathan Manning <pininforthefjords@gmail.com>
Co-authored-by: Jonathan Manning <pininforthefjords@gmail.com>
Co-authored-by: Jonathan Manning <pininforthefjords@gmail.com>
…iz.py Co-authored-by: Jonathan Manning <pininforthefjords@gmail.com>
…iz.py Co-authored-by: Jonathan Manning <pininforthefjords@gmail.com>
…iz.py Co-authored-by: Jonathan Manning <pininforthefjords@gmail.com>
…PCA orphans, fix versions.yml, rename clustervisualiation -> clustervisualization
…R to fix numba caching in Singularity
… imports, and KMean n_init stable
Co-authored-by: Jonathan Manning <pininforthefjords@gmail.com>
Co-authored-by: Jonathan Manning <pininforthefjords@gmail.com>
…d test assertions
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New module:
custom/clusteringDescription 📖
Applies K-means or DBSCAN clustering to
plink2_pcaeigenvec output.Input
eigenvecfromplink2_pca(coordinates + meta)algorithm:'kmeans'or'dbscan'n_clusters: K-means clusters (int)dbscan_eps,dbscan_min_samples: DBSCAN paramsOutput
*_clusters.csv: cluster assignments*_clustering_info.json: params used (optional)versions.ymlTest results ✅
nf-core modules lint custom/clusteringnf-test test custom/clustering/tests/main.nf.testpre-commitpassedDependencies
Container:
matplotlib_pandas_python_scikit-learn_pruned:054f91aaa56bd7d5Conda:
environment.ymlnf-core/modules version
4.0.0