c2v.tl.find_mnn

c2v.tl.find_mnn(clones, batch_key, use_rep='X_pca', k=10, k_trim=3, metric='euclidean', uns_key='simple_mnn', graph_key='mnn', progress_bar=True)

Find anchors between batches in clones.obs[batch_key] using MNNs using clones.obsm[use_rep].

Parameters:

clones AnnData

Annotated data matrix at the clone level.

batch_key str

Column in clones.obs containing batch information.

use_rep str, optional

Key in clones.obsm containing representation to use for anchor finding, by default “X_pca”.

k int, optional

Number of nearest neighbors to use for anchor finding, by default 10.

metric str, optional

Distance metric to use for anchor finding, by default “euclidean”.

uns_key str, optional

Key in clones.uns to store anchor information, by default “simple_mnn”.

graph_key str, optional

Key in clones.obsp to store MNN graph, by default “mnn”.

progress_bar bool, optional

Whether to show a progress bar, by default True.

k_trim int

Return type:

None

Returns:

None MNN graph is stored in clones.obsp[graph_key]. Anchor information is stored in clones.uns[uns_key].