spac.transformations.tsne(adata, layer=None, **kwargs)[source]

Perform t-SNE transformation on specific layer information.

Parameters:

  • adata (anndata.AnnData) – The AnnData object.

  • layer (str) – Layer for phenograph cluster calculation.

  • **kwargs – Parameters for scanpy.tl.tsne function.

Returns:

adata – Updated AnnData object with t-SNE coordinates.

Return type:

anndata.AnnData