Add_embed

Add embeddings for a Seurat object.

An efficient data integration method is provided for multiple spatial transcriptomics data with non-cluster-relevant effects such as the complex batch effects. It unifies spatial factor analysis simultaneously with spatial clustering and embedding alignment, requiring only partially shared cell/domain clusters across datasets. More details can be referred to Wei Liu, et al. (2023) <doi:10.1038/s41467-023-35947-w>.

Wei Liu

PRECAST

Embedding and Clustering with Alignment for Spatial Datasets

Yi Yang

Jin Liu

Add_embed function

<dl> <dt>embed</dt>
<dd>an embedding matrix.</dd> <dt>seu</dt>
<dd>a Seurat object.</dd> <dt>embed_name</dt>
<dd>an optional string, the name of embeddings.</dd> <dt>assay</dt>
<dd>Name of assay that that embed is being put</dd></dl>

Arguments

Author

Add embeddings for a Seurat object — Add_embed

<dl>

 <dt>embed</dt>
<dd>an embedding matrix.</dd>

 <dt>seu</dt>
<dd>a Seurat object.</dd>

 <dt>embed_name</dt>
<dd>an optional string, the name of embeddings.</dd>

 <dt>assay</dt>
<dd>Name of assay that that embed is being put</dd>

</dl>

Add_embed: Add embeddings for a Seurat object

Description

Usage

Value

Arguments

Author

Details

See Also