Addcoord2embed

Calculate the adjacency matrix given a spatial coordinate matrix with 2-dimension or 3-dimension or more.

A spatially-aware cell clustering algorithm is provided with cluster significance assessment. It comprises four key modules: spatially-aware cell-gene co-embedding, cell clustering, signature gene identification, and cluster significant assessment. More details can be referred to Peng Xie, et al. (2025) <doi:10.1016/j.cell.2025.05.035>.

Wei Liu

coFAST

Spatially-Aware Cell Clustering Algorithm with Cluster
Significant Assessment

Xiao Zhang

Yi Yang

Peng Xie

Chengqi Lin

Jin Liu

Addcoord2embed function

<dl><dt>seu</dt>
<dd>a SeuratObject with spatial coordinate information in the <code>meta.data</code> slot.</dd>
<dt>coord.name</dt>
<dd>a character vector, specify the names of spatial coordinates in the <code>meta.data</code> slot. For example, <code>c("x", "y")</code>.</dd>
<dt>assay</dt>
<dd>a string, specify the assay.</dd></dl>

Arguments

Add the spatial coordinates to the reduction slot — Addcoord2embed

<dl>

<dt>seu</dt>
<dd>a SeuratObject with spatial coordinate information in the <code>meta.data</code> slot.</dd>


<dt>coord.name</dt>
<dd>a character vector, specify the names of spatial coordinates in the <code>meta.data</code> slot. For example, <code>c("x", "y")</code>.</dd>


<dt>assay</dt>
<dd>a string, specify the assay.</dd>

</dl>

Addcoord2embed: Add the spatial coordinates to the reduction slot

Description

Usage

Value

Arguments

References

See Also

Examples