Is there a way to calculate variance for PCA analysis and elbow plot in Stereopy?

STOmics / Stereopy

A toolkit of spatial transcriptomic analysis.

MIT License

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Is there a way to calculate variance for PCA analysis and elbow plot in Stereopy? #175

Closed danammak closed 10 months ago

danammak commented 11 months ago

Hi Team,

I see that there is a following function: "StPipeline.pca(use_highly_genes=False, n_pcs=None, svd_solver='auto', hvg_res_key='highly_variable_genes', res_key='pca')"
to calculate Principal Components but how do I decide how many PCs I can consider further for downstream analysis. I could not find any function to calculate variance and plot elbow/scree plot. Please suggest me on this.

UglyRay7 commented 11 months ago

Currently, our tool does not support a ready-to-use plotting function for PCA elbow/scree plot which displays the contribution of PCs. Thanks for your feedback, and this function will be developed in a later version.

Ray