runIntegratedUMAP: Run integrated UMAP

In drieslab/Giotto_site_suite: Spatial Single-Cell Transcriptomics Toolbox

Run integrated UMAP

Description

Run integrated UMAP

Usage

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,
  ...
)

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
...	additional UMAP parameters

Value

A Giotto object with integrated UMAP

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