Multi omics integration with WNN

Multi omics integration with WNN

runWNN(
  gobject,
  spat_unit = "cell",
  feat_types = c("rna", "protein"),
  reduction_methods = c("pca", "pca"),
  reduction_names = c("rna.pca", "protein.pca"),
  k = 20,
  integrated_feat_type = NULL,
  matrix_result_name = NULL,
  w_names = c(NULL, NULL),
  verbose = FALSE
)

Arguments

gobject

A Giotto object with individual PCA feat_types pre-calculated

spat_unit

spatial unit

feat_types

feature types to integrate. Default = c("rna", "protein")

reduction_methods

reduction methods for each feature type. Default = c("pca", "pca")

reduction_names

names of the reduction methods to use. Default = c("rna.pca", "protein.pca")

k

number of neighbors to calculate cell distances, default = 20

integrated_feat_type

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

matrix_result_name

Default = 'theta_weighted_matrix'

w_names

optional. Names for the weighted matrices. If NULL, automatic names composed by w_feat_type will be created.

verbose

be verbose

Value

A Giotto object with a new multiomics slot containing the theta_weighted_matrix and individual weight matrices.