Run integrated UMAP

Run integrated UMAP

runIntegratedUMAP(
  gobject,
  spat_unit = "cell",
  modality1 = "rna",
  modality2 = "protein",
  integrated_feat_type = NULL,
  integration_method = "WNN",
  matrix_result_name = "theta_weighted_matrix",
  k = 20,
  spread = 5,
  min_dist = 0.01,
  force = FALSE,
  ...
)

Arguments

gobject

A giotto object

spat_unit

spatial unit

modality1

modality 1 name. Default = "rna"

modality2

modality 2 name. Default = "protein"

integrated_feat_type

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

integration_method

multiomics integration method used. Default = 'WNN'

matrix_result_name

Default = 'theta_weighted_matrix'

k

k number

spread

UMAP param: spread

min_dist

UMAP param: min_dist

force

force calculation of integrated kNN. Default = FALSE

...

additional UMAP parameters

Value

A Giotto object with integrated UMAP