runWNN: Multi omics integration with WNN

In drieslab/Giotto_site_suite: Spatial Single-Cell Transcriptomics Toolbox

Multi omics integration with WNN

Description

Multi omics integration with WNN

Usage

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
)

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

Value

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

drieslab/Giotto_site_suite documentation built on April 26, 2023, 11:51 p.m.