Multi omics integration with WNN

Source: R/wnn.R

Multi omics integration with WNN

runWNN(
  gobject,
  spat_unit = "cell",
  modality_1 = "rna",
  modality_2 = "protein",
  pca_name_modality_1 = "rna.pca",
  pca_name_modality_2 = "protein.pca",
  k = 20,
  integrated_feat_type = NULL,
  matrix_result_name = NULL,
  w_name_modality_1 = NULL,
  w_name_modality_2 = NULL,
  verbose = FALSE
)

Arguments

gobject

A Giotto object with individual PCA modalities pre-calculated

spat_unit

spatial unit

modality_1

modality 1 name. Default = "rna"

modality_2

modality 2 name. Default = "protein"

pca_name_modality_1

Default = 'rna.pca'

pca_name_modality_2

Default = 'protein.pca'

k

k number, default = 20

integrated_feat_type

integrated feature type (e.g. 'rna_protein')

matrix_result_name

Default = 'theta_weighted_matrix'

w_name_modality_1

name for modality 1 weights

w_name_modality_2

name for modality 2 weights

verbose

be verbose

Value

A Giotto object with integrated UMAP (integrated.umap) within the dimension_reduction slot and Leiden clusters (integrated_leiden_clus) in the cellular metadata.