Jointly measured spatial omic assays territories
Usage
joint_territories(
mod1,
mod2,
dimensions = seq(1, 30),
embedding = "last",
method = "interlace",
norm_method = "log_norm",
dim_reduction = "PCA",
signal = "variable_features",
verbose = TRUE
)Arguments
- mod1
vesalius_assay object containing first modality
- mod2
vesalius_assay objecty containing second modality
- dimensions
numeric vector describing latent space dimensions to use during intergration
- method
character - integration method. interlace - mean - concat are available options
- norm_method
character - which count values should be use for integration when using concat method
- dim_reduction
characater - which dim reduction methods should be used for concat integration (PCA,PCA_L,UMAP,LSI,LSI_UMAP,NMF)
- verbose
logical - should progress message be outputed to the console.