random-walk-graph-laplacian-smoothing

Demo scanpy-native implementation of random-walk graph laplacian smoothing for single-cell transcriptomics data.

Background

doc/RW_graph_laplacian_smoothing.pdf

Usage

from graph_laplacian import RWGLSmooth

rw_smoother = RWGLSmooth(
    adata,
    alpha=0.05, # diffusion coefficient
)

rw_smoother.step(
    feature_matrix=adata.X,
    steps=10,
    key_added='X_rw_smooth_10_steps', # added to adata.layers
    in_place=True,
    verbose=True,
)