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Create a spatial Delaunay network
createSpatialDelaunayNetwork.Rd
Create a spatial Delaunay network based on cell centroid physical distances.
Usage
createSpatialDelaunayNetwork(
gobject,
name = "Delaunay_network",
spat_unit = NULL,
feat_type = NULL,
spat_loc_name = NULL,
method = c("deldir", "delaunayn_geometry", "RTriangle"),
dimensions = "all",
maximum_distance = "auto",
minimum_k = 0,
options = "Pp",
Y = TRUE,
j = TRUE,
S = 0,
verbose = T,
return_gobject = TRUE,
output = c("spatialNetworkObj", "data.table"),
...
)
Arguments
- gobject
giotto object
- name
name for spatial network (default = 'delaunay_network')
- spat_unit
spatial unit
- feat_type
feature type
- spat_loc_name
name of spatial locations
- 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)
- maximum_distance
distance cuttof for Delaunay neighbors to consider. If "auto", "upper whisker" value of the distance vector between neighbors is used; see the boxplotgraphics documentation for more details.(default = "auto")
- minimum_k
minimum number of neighbours if maximum_distance != NULL
- options
(geometry) String containing extra control options for the underlying Qhull command; see the Qhull documentation 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
be verbose
- return_gobject
logical. return giotto object (default = TRUE)
- output
character. Object type to return spatial network as when
return_gobject = FALSE
. (default: 'spatialNetworkObj')- ...
Other additional parameters
Details
Creates a spatial Delaunay network as explained in delaunayn
(default), deldir
, or triangulate
.