scgenome.tl.compute_umap

scgenome.tl.compute_umap(adata, layer_name='copy', n_components=2, n_neighbors=15, min_dist=0.1, metric='euclidean')

Cluster cells by copy number.

Parameters:

• adata (AnnData) – copy number data

• layer_name (str, optional) – layer with copy number data on which to perform umap dimensionality reduction, None for X, by default ‘copy’

• n_components (int) – umap n_components param

• n_neighbors (int) – umap n_neighbors param

• min_dist (float) – umap min_dist param

Returns:

copy number data with additional umap_1, umap_2 columns

Return type:

AnnData