Add UMAP embeddings for a Seurat object — AddUMAP • PRECAST

Run UMAP dimensionality reduction on selected features.

AddUMAP(seuInt, n_comp=3, reduction='PRECAST', assay='PRE_CAST', seed=1)

Arguments

seuInt: a Seurat object.
n_comp: an optional positive integer, specify the number of features to be extracted.
reduction: an optional string, means which dimensional reduction (e.g. PRECAST, PCA) to use for the UMAP. Default is PRECAST.
assay: Name of assay that that t-SNE is being run on.
seed: an optional integer, the random seed to evaluate UMAP.

Details

Nothing

Value

Return a revised Seurat object by adding UMAP reduction object.

Author

Wei Liu

Note

nothing

See also

None