The NodeDimReduc class

The NodeDimReduc class stores a dimensionality reduction computed on the nodes of a CellGraph. It follows the same design as DimReduc: a required embeddings matrix, optional feature loadings, standard deviations, a dimension key, and a miscellaneous list for method-specific extras.

Slots

embeddings

A numeric matrix of node embeddings (nodes x dimensions). Row names are node names when the object is created. When the reduction is stored on a CellGraph, embedding rows follow the graph nodes map and row names are dropped.

loadings

An optional numeric matrix of feature loadings (features x dimensions)

stdev

A numeric vector of standard deviations (or eigenvalues) for each dimension

key

A character scalar used as the column-name prefix, ending with _ (for example "PC_")

method

A character scalar naming the reduction method (for example "pca" or "umap")

misc

A named list of unstructured additional data