concat_embed: create new embedding from jointly measure spatial omics

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

create new embedding from jointly measure spatial omics

Description

create new embedding from jointly measure spatial omics

Usage

concat_embed(seed, query, dimensions, norm_method, dim_reduction, signal)

Arguments

seed	vesalius_assay object of the first modality
query	vesalius_assay object of the second modality
dimensions	int - number of gray scale images to create
norm_method	string describing which normalisation method to use. One of the following "log_norm", "SCT", "TFIDF", "raw"
dim_reduction	string describing which dimensionality reduction method should be used. One of the following: "PCA", "PCA_L", "UMAP", "LSI", "LSI_UMAP"

Details

Create new latent space using feature from both modalities Creates a new feature matrix than in nromalized and converted to latent space image stack.

Value

embedding matrix used as grey scale image stack

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