Split cluster annotations based on a spatial network

identifyTMAcores(
  gobject,
  spat_unit = NULL,
  feat_type = NULL,
  spatial_network_name = "Delaunay_network",
  core_id_name = "core_id",
  id_fmt = "%d",
  include_all_ids = TRUE,
  missing_id_name = "not_connected",
  min_nodes = 5,
  join_split_cores = TRUE,
  join_tolerance = 1.2,
  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
core_id_name: metadata column name for the core information
id_fmt: character. [sprintf] formatting to use for core ids
include_all_ids: logical. Include all ids, including vertex ids not found in the spatial network
missing_id_name: character. Name for nodes that are not connected to a core.
min_nodes: numeric. Minimal number of nodes to not be considered an unconnected group.
join_split_cores: logical. Attempt to repair core IDs when a core is split down the middle and detected as two different cores.
join_tolerance: numeric. Max ratio allowed relative to previous max core convex hull area when determining if a pair of cores should be joined.
return_gobject: logical. Return giotto object

Value

cluster annotations