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,
...
)giotto object
name for spatial network (default = 'spatial_network')
which spatial dimensions to use (default = all)
which method to use to create a spatial network. (default = Delaunay)
Delaunay method to use
distance cuttof for nearest neighbors to consider for Delaunay network
(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)
(RTriangle) If TRUE prohibits the insertion of Steiner points on the mesh boundary.
(RTriangle) If TRUE jettisons vertices that are not part of the final triangulation from the output.
(RTriangle) Specifies the maximum number of added Steiner points.
minimum nearest neigbhours if maximum_distance != NULL
method to create kNN network
number of nearest neighbors based on physical distance
distance cuttof for nearest neighbors to consider for kNN network
verbose
boolean: return giotto object (default = TRUE)
Additional parameters for the selected function
giotto object with updated spatial network slot
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