Split cluster annotations based on a spatial network

spatialSplitCluster(
  gobject,
  spat_unit = NULL,
  feat_type = NULL,
  spatial_network_name = "Delaunay_network",
  cluster_col,
  split_clus_name = paste0(cluster_col, "_split"),
  missing_id_name = "not_connected",
  return_gobject = TRUE
)

Arguments

gobject: giotto object
spat_unit: spatial unit (e.g. "cell")
feat_type: feature type (e.g. "rna", "dna", "protein")
spatial_network_name: character. Name of spatial network to use
cluster_col: character. Column in metadata containing original clustering
split_clus_name: character. Name to assign the split cluster results
return_gobject: logical. Return giotto object
include_all_ids: logical. Include all ids, including vertex ids not found in the spatial network

Value

giotto object with cluster annotations

Examples

g <- GiottoData::loadGiottoMini("vizgen")
#> 1. read Giotto object
#> 2. read Giotto feature information
#> 3. read Giotto spatial information
#> 3.1 read Giotto spatial shape information
#> 3.2 read Giotto spatial centroid information
#> 3.3 read Giotto spatial overlap information
#> 4. read Giotto image information
#> python already initialized in this session
#>  active environment : '/usr/bin/python3'
#>  python version : 3.10
#> checking default envname 'giotto_env'
#> a system default python environment was found
#> Using python path:
#>  "/usr/bin/python3"
activeSpatUnit(g) <- "aggregate"
spatPlot2D(g, cell_color = "leiden_clus")


g <- spatialSplitCluster(g,
    cluster_col = "leiden_clus",
    split_clus_name = "new"
)
# don't show legend since there are too many categories generated
spatPlot2D(g, cell_color = "new", show_legend = FALSE)