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Starlitnightly / omicverse

A python library for multi omics included bulk, single cell and spatial RNA-seq analysis.
https://starlitnightly.github.io/omicverse/
GNU General Public License v3.0
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GaussianMixture: mclust_py() got an unexpected keyword argument 'covariance_type' #127

Closed muyu-fudan closed 2 weeks ago

muyu-fudan commented 1 month ago

when i set method='GMM' to cluster the cells , the error occured. how can i use the Gaussian mixture model clustering image image image

Starlitnightly commented 1 month ago

The principle of mcluster is GMM, and the relevant parameters have been modified to similar parameters of mcluster. The old tutorial has not been updated yet, and you can check the source code to confirm the optional parameters

yanbosmu commented 2 days ago

any solution to this?

yanbosmu commented 2 days ago

ov.utils.cluster(adata, use_rep='scaled|original|X_pca', method='GMM', n_components=21) # Removed 'covariance_type' and 'tol'