scglue.data.transfer_labels
- scglue.data.transfer_labels(ref, query, field, n_neighbors=30, use_rep=None, key_added=None, **kwargs)[源代码]
Transfer discrete labels from reference dataset to query dataset
- 参数:
ref (
AnnData
) – Reference datasetquery (
AnnData
) – Query datasetfield (
str
) – Field to be transferred inref.obs
(must be discrete)n_neighbors (
int
) – Number of nearest neighbors used for label transferuse_rep (
typing.Optional
[str
]) – Data representation based on which to find nearest neighbors, by default uses{ref, query}.X
.key_added (
typing.Optional
[str
]) – Newquery.obs
key added for the transfered labels, by default the same asfield
.**kwargs – Additional keyword arguments are passed to
sklearn.neighbors.NearestNeighbors
- 返回类型:
备注
First, nearest neighbors between reference and query cells are searched and weighted by Jaccard index of SNN (shared nearest neighbors). The Jaccard indices are then normalized per query cell to form a mapping matrix. To obtain predictions for query cells, we multiply the above mapping matrix to the one-hot matrix of reference labels. The category with the highest score is taken as the final prediction, while its score is interpreted as transfer confidence (stored as “{key_added}_confidence” in
query.obs
).