embed in grey scale using latent semantic indexing
followed by UMAP
Usage
embed_lsi_umap(
counts,
dimensions,
features = NULL,
remove_lsi_1,
verbose = TRUE
)
Arguments
- counts
Seurat object containing normalised counts
- dimensions
numeric for number of latent space dimensions to use
- features
custom vector of features
- remove_lsi_1
logical if first LSI dimenions should be removed
- verbose
logical if progress messages should be outputed
Value
normalised LSI embedding matrix