Usage

Quick start

The scbiot class wraps the full preprocessing + embedding pipeline. Pass anndata object.

import numpy as np
import pandas as pd
import scbiot import scb
import scanpy as sc

# Use optimal transport for prealignment
adata = sc.read_h5ad('alldata.h5ad')
)
adata, metrics = scb.ot.integrate(
        adata,
        preset="rna",
        obsm_key="X_pca",
        batch_key="batch",
        out_key="X_ot",
    )
    print(metrics)

# Use OT embeddings for downstream analysis
sc.pp.neighbors(adata, use_rep='X_ot')
sc.tl.umap(adata)
sc.tl.leiden(adata, resolution=0.8, key_added='leiden_X_ot')
adata