mioXpektron.analysis.embeddings

Nonlinear and linear sample embeddings for exploratory analysis.

Functions

compute_pca(X_scaled, y, savepath, *[, ...])	PCA embedding with variance ratio metadata.
compute_tsne(X_scaled, y, savepath, *[, ...])	t-SNE embedding via scikit-learn.
compute_umap(X_scaled, y, savepath, *[, ...])	UMAP embedding when umap-learn is installed.
resolve_embedding_methods(*[, ...])	Resolve the list of embedding methods to compute.
run_embeddings(X_scaled, y, outdir, *[, ...])	Compute and save requested embeddings; return coordinate arrays.

mioXpektron.analysis.embeddings.resolve_embedding_methods(*, embedding_methods=None, run_umap=False, run_tsne=False)

Resolve the list of embedding methods to compute.

Parameters:

• embedding_methods (Sequence[str] | None)

• run_umap (bool)

• run_tsne (bool)

Return type:

List[str]

mioXpektron.analysis.embeddings.compute_pca(X_scaled, y, savepath, *, random_state=0)

PCA embedding with variance ratio metadata.

Parameters:

• X_scaled (ndarray)

• y (Series)

• savepath (str)

• random_state (int)

Return type:

Tuple[ndarray, ndarray]

mioXpektron.analysis.embeddings.compute_umap(X_scaled, y, savepath, *, n_neighbors=15, min_dist=0.1, random_state=0)

UMAP embedding when umap-learn is installed.

Parameters:

• X_scaled (ndarray)

• y (Series)

• savepath (str)

• n_neighbors (int)

• min_dist (float)

• random_state (int)

Return type:

ndarray | None

mioXpektron.analysis.embeddings.compute_tsne(X_scaled, y, savepath, *, perplexity=30.0, learning_rate='auto', random_state=0)

t-SNE embedding via scikit-learn.

Parameters:

• X_scaled (ndarray)

• y (Series)

• savepath (str)

• perplexity (float)

• learning_rate (str | float)

• random_state (int)

Return type:

ndarray

mioXpektron.analysis.embeddings.run_embeddings(X_scaled, y, outdir, *, methods=None, run_umap=False, run_tsne=False, random_state=0, umap_n_neighbors=15, umap_min_dist=0.1, tsne_perplexity=30.0)

Compute and save requested embeddings; return coordinate arrays.

Parameters:

• X_scaled (ndarray)

• y (Series)

• outdir (str)

• methods (Sequence[str] | None)

• run_umap (bool)

• run_tsne (bool)

• random_state (int)

• umap_n_neighbors (int)

• umap_min_dist (float)

• tsne_perplexity (float)

Return type:

Dict[str, ndarray]