Create a spatial Delaunay network based on cell centroid physical distances.
createSpatialDelaunayNetwork( gobject, method = c("deldir", "delaunayn_geometry", "RTriangle"), dimensions = "all", name = "Delaunay_network", maximum_distance = "auto", minimum_k = 0, options = "Pp", Y = TRUE, j = TRUE, S = 0, verbose = T, return_gobject = TRUE, ... )
| gobject | giotto object |
|---|---|
| method | package to use to create a Delaunay network |
| dimensions | which spatial dimensions to use. Use "sdimx" (spatial dimension x), "sdimy", "sdimz" respectively to refer to X (or the 1st), Y (or the 2nd) and Z(or the 3rd) dimension, see details. (default = all) |
| name | name for spatial network (default = 'delaunay_network') |
| maximum_distance | distance cuttof for Delaunay neighbors to consider. If "auto", "upper wisker" value of the distance vector between neighbors is used; see the boxplotgraphics documentation for more details.(default = "auto") |
| minimum_k | minimum number of neigbhours if maximum_distance != NULL |
| 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. |
| verbose | verbose |
| return_gobject | boolean: return giotto object (default = TRUE) |
| ... | Other additional parameters |
giotto object with updated spatial network slot
Creates a spatial Delaunay network as explained in delaunayn (default), deldir, or triangulate.