embed_latent_space: embed latent space

In patrickCNMartin/Vesalius: Vesalius: Dissecting Tissue Anatomy from Spatial Transcriptomic Data

embed latent space

Description

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

Details

General method dispatch function for dim reduction methods

Value

data frame of normalised embedding values.

patrickCNMartin/Vesalius documentation built on April 17, 2025, 11:31 p.m.