This function performs a co-embedding UMAP of both gene and cell embeddings from a Seurat object. It integrates the dimensionality reduction results for genes and cells into a shared UMAP space.
CoUMAP(
seu,
reduction = "caesar",
reduction.name = "caesarUMAP",
gene.set = NULL,
slot = "data",
assay = "RNA",
seed = 1,
...
)A modified Seurat object with the co-embedding UMAP stored in the specified reduction.name slot.
A Seurat object containing the single-cell RNA-seq data.
A character string specifying the name of the dimensional reduction to use (e.g., "caesar"). Default is "caesar".
A character string specifying the name of the new dimensional reduction slot in the Seurat object where the co-embedding UMAP will be stored. Default is "caesarUMAP".
A character vector specifying the set of genes to include in the co-embedding. If NULL, all genes are used. Default is NULL.
A character string specifying the slot in the Seurat object to use for gene expression data. Default is "data".
A character string specifying the assay to use. Default is "RNA".
An integer specifying the random seed for reproducibility. Default is 1.
Additional arguments passed to scater::calculateUMAP.
The function extracts the embeddings for both genes and cells from the specified dimensional reduction, combines them, and computes a UMAP embedding. The resulting co-embedding UMAP is stored in a new dimensional reduction slot in the Seurat object.
calculateUMAP for UMAP calculation.
data(toydata)
seu <- toydata$seu
seu <- CoUMAP(seu, gene.set = rownames(seu))
print(seu)
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