kaleidocell.recompute_pca_umap#

kaleidocell.recompute_pca_umap(adata, n_pcs=50, umap_min_dist=0.5, umap_spread=1.0, random_state=42)[source]#

Recompute PCA and UMAP on adata in-place.

Parameters:

  • adata (AnnData) – Annotated data matrix.

  • n_pcs (int, default 50) – Number of principal components.

  • umap_min_dist (float, default 0.5) – UMAP min_dist parameter.

  • umap_spread (float, default 1.0) – UMAP spread parameter.

  • random_state (int, default 42) – Random seed for reproducibility.

Returns:

The same adata object with updated obsm["X_pca"] and obsm["X_umap"].

Return type:

AnnData