createSpatialNetwork

Create a spatial network based on cell centroid physical distances.

createSpatialNetwork(
  gobject,
  name = NULL,
  dimensions = "all",
  method = c("Delaunay", "kNN"),
  delaunay_method = c("deldir", "delaunayn_geometry", "RTriangle"),
  maximum_distance_delaunay = "auto",
  options = "Pp",
  Y = TRUE,
  j = TRUE,
  S = 0,
  minimum_k = 0,
  knn_method = "dbscan",
  k = 4,
  maximum_distance_knn = NULL,
  verbose = F,
  return_gobject = TRUE,
  ...
)

Arguments

gobject	giotto object
name	name for spatial network (default = 'spatial_network')
dimensions	which spatial dimensions to use (default = all)
method	which method to use to create a spatial network. (default = Delaunay)
delaunay_method	Delaunay method to use
maximum_distance_delaunay	distance cuttof for nearest neighbors to consider for Delaunay network
options	(geometry) String containing extra control options for the underlying Qhull command; see the Qhull documentation (../doc/qhull/html/qdelaun.html) for the available options. (default = 'Pp', do not report precision problems)
Y	(RTriangle) If TRUE prohibits the insertion of Steiner points on the mesh boundary.
j	(RTriangle) If TRUE jettisons vertices that are not part of the final triangulation from the output.
S	(RTriangle) Specifies the maximum number of added Steiner points.
minimum_k	minimum nearest neigbhours if maximum_distance != NULL
knn_method	method to create kNN network
k	number of nearest neighbors based on physical distance
maximum_distance_knn	distance cuttof for nearest neighbors to consider for kNN network
verbose	verbose
return_gobject	boolean: return giotto object (default = TRUE)
...	Additional parameters for the selected function

Value

giotto object with updated spatial network slot

Details

Creates a spatial network connecting single-cells based on their physical distance to each other. For Delaunay method, neighbors will be decided by delaunay triangulation and a maximum distance criteria. For kNN method, number of neighbors can be determined by k, or maximum distance from each cell with or without setting a minimum k for each cell.

dimensions: default = 'all' which takes all possible dimensions. Alternatively you can provide a character vector that specififies the spatial dimensions to use, e.g. c("sdimx', "sdimy") or a numerical vector, e.g. 2:3