load_nc_connectivity — load_nc_connectivity • Giotto

load niche cluster connectivity

load_nc_connectivity(
  gobject,
  ontrac_results_dir = getwd(),
  GNN_dir = file.path(ontrac_results_dir, "GNN_dir"),
  spat_unit = "niche cluster",
  feat_type = "connectivity",
  name = "normalized"
)

Arguments

gobject: giotto object
ontrac_results_dir: the directory where the ONTraC results are saved. Default is getwd()
GNN_dir: the directory to save the GNN results. Default is file.path(ontrac_results_dir, "GNN_dir")
spat_unit: spatial unit (e.g. "cell")
feat_type: feature type (e.g. "rna", "dna", "protein")
name: name for the connectivity matrix

Value

gobject with niche cluster connectivity matrix

Details

This function loads the ONTraC outputed niche cluster connectivity matrix as an exprObj into the giotto object.