Embed latent space into grey color scale.
Usage
embed_latent_space(
counts,
assay,
dim_reduction,
dimensions,
features = NULL,
remove_lsi_1,
verbose
)Arguments
- counts
Seurat object containing counts (generally normalised)
- assay
charcter string of the assay being used
- dim_reduction
dimensionality reduction method that will be used Select from PCA, PCA_L, UMAP, LSI, LSI_UMAP
- dimensions
numeric for number of dimeniosn top retain after dimensionality reduction
- features
custom features used for dim reduction
- remove_lsi_1
logical if first dimension of LSI embedding should be removed (will soon be depreciated)
- verbose
logical if progress messages should be outputed or not